From jk435 at njit.edu Thu Sep 3 21:02:17 2020 From: jk435 at njit.edu (Jatin Kashyap) Date: Fri, 4 Sep 2020 00:02:17 -0400 Subject: ADL: "Unknown or inappropriate tag" Error in Vina for Protein File Message-ID: <89F5D506-A8F7-4F9C-9EF3-5C9720156D33@njit.edu> Dear AutoDock Community, Please redirect me if I am posting to the wrong email list. I am getting a file format error in the Vina docking run.[1] I am taking a protein and trimming it in PyMol followed by minimization on YASARA server. I am saving YASARA output as .pdbqt, but since it contains branch information as well so Vina was throwing error. I was suggested by YASARA support team to pass it through open babel and then save it as .pdbqt to get rid of branch information by using the appropriate flag. I did exactly according to that. But upon looking into the resultant file, it seems like it has multiple models in the file with corresponding tags, which Vina is not able to identify and hence throwing an error.[1] I am attaching my protein file here.[2] Can anybody please help me understand how to fix it given my few months of experience with docking simulations. Thank you very much. [1] Output will be ZINC000589822496_out.pdbqt Reading input ... Parse error on line 3059 in file ""6w9c_+.pdbqt"": Unknown or inappropriate tag [2] ?? Jatin Kashyap Ph.D. Student Department of Mechanical and Industrial Engineering New Jersey Institute of Technology (NJIT) University Heights Newark, NJ 07102-1982 Phone- (201)889-5783 Email- jk435 at njit.edu From carmen.esposito at phys.chem.ethz.ch Fri Sep 4 01:41:02 2020 From: carmen.esposito at phys.chem.ethz.ch (Esposito Carmen) Date: Fri, 4 Sep 2020 08:41:02 +0000 Subject: ADL: prepare_ligand4.py converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion Message-ID: <12139b146370456d8bfc01bf1aa274ff@phys.chem.ethz.ch> Hi! I am using the python script prepare_ligand4.py to convert mol2 files to pdbqt (I generate the mol2 files containing partial charges using antechamber of AmberTools20). pythonsh prepare_ligand4.py -l file.mol2 -C -o file.pdbqt However, I noticed that when doing the format conversion carbon atoms with the atom type CA (in the mol2) are transformed into calcium atoms (Ca, in the pdbqt file). I attached here a couple of examples. Is it possible that this is a bug? Thank you very much for your help! Best regards, Carmen -------------- next part -------------- A non-text attachment was scrubbed... Name: 3R1_pH74_netcharge.mol2 Type: application/octet-stream Size: 6017 bytes Desc: 3R1_pH74_netcharge.mol2 URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 3R1_pH74_netcharge.pdbqt Type: application/octet-stream Size: 3624 bytes Desc: 3R1_pH74_netcharge.pdbqt URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: CKO_pH74_netcharge.mol2 Type: application/octet-stream Size: 8627 bytes Desc: CKO_pH74_netcharge.mol2 URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: CKO_pH74_netcharge.pdbqt Type: application/octet-stream Size: 4687 bytes Desc: CKO_pH74_netcharge.pdbqt URL: From hvandam at bnl.gov Fri Sep 4 06:38:01 2020 From: hvandam at bnl.gov (Van Dam, Hubertus) Date: Fri, 4 Sep 2020 13:38:01 +0000 Subject: ADL: prepare_ligand4.py converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion Message-ID: <20758663-5A41-4BA5-9488-2963693F6710@bnl.gov> Hi Carmen, Where did you get the mol2 files from? In MOL2 files (see: http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf) the atom types are supposed to be SYBYL atom types. I guess the alpha-carbons should be sp3 carbons (in most cases?) which would be indicated with C.3 (see: http://tccc.iesl.forth.gr/education/local/quantum/molecular_modeling/guide_documents/SYBYL_data_document.html). The atom type ca is actually Calcium. So I think the script is converting the MOL2 files correctly as far as I can see, it is just that the MOL2 files don't specify the structure as it should. Best wishes, Huub ----------------------------------------------------------------------------------------------------- Hubertus van Dam, 631-344-6020, hvandam at bnl.gov Brookhaven National Laboratory ?On 9/4/20, 04:59, "autodock-bounces at scripps.edu on behalf of Esposito Carmen" wrote: Hi! I am using the python script prepare_ligand4.py to convert mol2 files to pdbqt (I generate the mol2 files containing partial charges using antechamber of AmberTools20). pythonsh prepare_ligand4.py -l file.mol2 -C -o file.pdbqt However, I noticed that when doing the format conversion carbon atoms with the atom type CA (in the mol2) are transformed into calcium atoms (Ca, in the pdbqt file). I attached here a couple of examples. Is it possible that this is a bug? Thank you very much for your help! Best regards, Carmen From carmen.esposito at phys.chem.ethz.ch Fri Sep 4 07:21:44 2020 From: carmen.esposito at phys.chem.ethz.ch (Esposito Carmen) Date: Fri, 4 Sep 2020 14:21:44 +0000 Subject: ADL: prepare_ligand4.py converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion In-Reply-To: <20758663-5A41-4BA5-9488-2963693F6710@bnl.gov> References: <20758663-5A41-4BA5-9488-2963693F6710@bnl.gov> Message-ID: Hi, Thank you for your reply. In the mol2, the atom named CA has the correct type c3 (and also the 3D structure is correct). 9 CA 5.9540 0.3730 -0.1620 c3 1 UNK 0.174500 The problem occurs only when I do the format conversion. In the pdbqt: ATOM 18 CA UNK d 1 5.954 0.373 -0.162 0.00 0.00 0.174 Ca ...All other carbon atoms named C1, C2, C3... are correctly recognised. So far, I corrected this error manually by modifying the line above, i.e. adjust the spacing between 18 and CA and replace "Ca" with "Ca". ATOM 18 CA UNK d 1 5.954 0.373 -0.162 0.00 0.00 0.174 C Anyway, I generated the mol2 file using the antechamber program from AmberTools20. After docking, I need to run MD simulations and this is why I parametrise the molecules in the first step. In this way, I can also use the same partial charges for docking. Best wishes, Carmen ________________________________ From: autodock-bounces at scripps.edu on behalf of Van Dam, Hubertus Sent: Friday, September 4, 2020 3:38:01 PM To: autodock at scripps.edu Subject: Re: ADL: prepare_ligand4.py converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion Hi Carmen, Where did you get the mol2 files from? In MOL2 files (see: http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf) the atom types are supposed to be SYBYL atom types. I guess the alpha-carbons should be sp3 carbons (in most cases?) which would be indicated with C.3 (see: http://tccc.iesl.forth.gr/education/local/quantum/molecular_modeling/guide_documents/SYBYL_data_document.html). The atom type ca is actually Calcium. So I think the script is converting the MOL2 files correctly as far as I can see, it is just that the MOL2 files don't specify the structure as it should. Best wishes, Huub ----------------------------------------------------------------------------------------------------- Hubertus van Dam, 631-344-6020, hvandam at bnl.gov Brookhaven National Laboratory ?On 9/4/20, 04:59, "autodock-bounces at scripps.edu on behalf of Esposito Carmen" wrote: Hi! I am using the python script prepare_ligand4.py to convert mol2 files to pdbqt (I generate the mol2 files containing partial charges using antechamber of AmberTools20). pythonsh prepare_ligand4.py -l file.mol2 -C -o file.pdbqt However, I noticed that when doing the format conversion carbon atoms with the atom type CA (in the mol2) are transformed into calcium atoms (Ca, in the pdbqt file). I attached here a couple of examples. Is it possible that this is a bug? Thank you very much for your help! Best regards, Carmen ________________________________________________ --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list --- From halkidesc at uncw.edu Fri Sep 4 07:52:25 2020 From: halkidesc at uncw.edu (Halkides, Christopher) Date: Fri, 4 Sep 2020 14:52:25 +0000 Subject: ADL: Covalent docking and the interpretation of a dissociation constant Message-ID: Hello Everyone, We have been mainly performing covalent docking. We are trying to interpret the value of K(eq) and ?G? that the program provides. For a noncovalent dock, the meaning of these two is clear, but I am unsure of the interpretation when covalent docking has been performed. Chris From hvandam at bnl.gov Fri Sep 4 08:32:45 2020 From: hvandam at bnl.gov (Van Dam, Hubertus) Date: Fri, 4 Sep 2020 15:32:45 +0000 Subject: ADL: prepare_ligand4.py converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion Message-ID: Hi Carmen, Sorry, I was looking at atoms 2, 3, and 4 in 3R1_pH74_netcharge.mol2. They are listed as: 2 C1 2.1330 -2.3280 0.5080 ca 1 UNK 0.502600 3 C2 1.3340 -1.2480 0.8230 ca 1 UNK -0.458600 4 C3 1.9460 -0.0180 0.9010 ca 1 UNK 0.698200 So the atom ids are fine (column 2) but the atom types are wrong (column 6). But you are right atom 9 as you stated: 9 CA 5.9540 0.3730 -0.1620 c3 1 UNK 0.174500 has the correct atom type but is erroneously converted into a Calcium atom. The observations of the both of us agree that the prepare_ligand4.py script determines the atom type from the atom id and incorrectly ignores the atom type. Fixing this problem by going by the atom type will break what the code does for atoms 2-4. However, in your examples it should be sufficient if the script checked the atom type when the atom id is ambiguous. Typical atom ids causing trouble are: CA CD CE CF (? I seem to remember this one but don't have an example for it right now) HO (occurs in Amber or Charmm , means Hydrogen attached to Oxygen, not Holmium) I think these are the most common troublemakers. Best wishes, Huub ----------------------------------------------------------------------------------------------------- Hubertus van Dam, 631-344-6020, hvandam at bnl.gov Brookhaven National Laboratory ?On 9/4/20, 10:38, "autodock-bounces at scripps.edu on behalf of Esposito Carmen" wrote: Hi, Thank you for your reply. In the mol2, the atom named CA has the correct type c3 (and also the 3D structure is correct). 9 CA 5.9540 0.3730 -0.1620 c3 1 UNK 0.174500 The problem occurs only when I do the format conversion. In the pdbqt: ATOM 18 CA UNK d 1 5.954 0.373 -0.162 0.00 0.00 0.174 Ca ...All other carbon atoms named C1, C2, C3... are correctly recognised. So far, I corrected this error manually by modifying the line above, i.e. adjust the spacing between 18 and CA and replace "Ca" with "Ca". ATOM 18 CA UNK d 1 5.954 0.373 -0.162 0.00 0.00 0.174 C Anyway, I generated the mol2 file using the antechamber program from AmberTools20. After docking, I need to run MD simulations and this is why I parametrise the molecules in the first step. In this way, I can also use the same partial charges for docking. Best wishes, Carmen ________________________________ From: autodock-bounces at scripps.edu on behalf of Van Dam, Hubertus Sent: Friday, September 4, 2020 3:38:01 PM To: autodock at scripps.edu Subject: Re: ADL: prepare_ligand4.py converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion Hi Carmen, Where did you get the mol2 files from? In MOL2 files (see: https://urldefense.com/v3/__http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf__;!!P4SdNyxKAPE!WFeaSGPsDp6rIP35Id41VTgGAH4PixH8zqZ3Q8gUvQHg3DFEMHBaNYTDBApG5Es$ ) the atom types are supposed to be SYBYL atom types. I guess the alpha-carbons should be sp3 carbons (in most cases?) which would be indicated with C.3 (see: https://urldefense.com/v3/__http://tccc.iesl.forth.gr/education/local/quantum/molecular_modeling/guide_documents/SYBYL_data_document.html__;!!P4SdNyxKAPE!WFeaSGPsDp6rIP35Id41VTgGAH4PixH8zqZ3Q8gUvQHg3DFEMHBaNYTDODoQzyQ$ ). The atom type ca is actually Calcium. So I think the script is converting the MOL2 files correctly as far as I can see, it is just that the MOL2 files don't specify the structure as it should. Best wishes, Huub ----------------------------------------------------------------------------------------------------- Hubertus van Dam, 631-344-6020, hvandam at bnl.gov Brookhaven National Laboratory On 9/4/20, 04:59, "autodock-bounces at scripps.edu on behalf of Esposito Carmen" wrote: Hi! I am using the python script prepare_ligand4.py to convert mol2 files to pdbqt (I generate the mol2 files containing partial charges using antechamber of AmberTools20). pythonsh prepare_ligand4.py -l file.mol2 -C -o file.pdbqt However, I noticed that when doing the format conversion carbon atoms with the atom type CA (in the mol2) are transformed into calcium atoms (Ca, in the pdbqt file). I attached here a couple of examples. Is it possible that this is a bug? Thank you very much for your help! Best regards, Carmen ________________________________________________ --- ADL: AutoDock List --- https://urldefense.com/v3/__http://autodock.scripps.edu/mailing_list__;!!P4SdNyxKAPE!WFeaSGPsDp6rIP35Id41VTgGAH4PixH8zqZ3Q8gUvQHg3DFEMHBaNYTD77H6UPM$ --- ________________________________________________ --- ADL: AutoDock List --- https://urldefense.com/v3/__http://autodock.scripps.edu/mailing_list__;!!P4SdNyxKAPE!WFeaSGPsDp6rIP35Id41VTgGAH4PixH8zqZ3Q8gUvQHg3DFEMHBaNYTD77H6UPM$ --- From carmen.esposito at phys.chem.ethz.ch Sat Sep 5 02:45:26 2020 From: carmen.esposito at phys.chem.ethz.ch (Esposito Carmen) Date: Sat, 5 Sep 2020 09:45:26 +0000 Subject: ADL: prepare_ligand4.py converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion In-Reply-To: References: Message-ID: Hi Huub, Yes, exactly. I think now that it is actually an atom type incompatibility. Because, even if C1, C2, and C3 have the atom type ca instead of c.ar, they are correctly recognized by antechamber as aromatic. Indeed, in the @BOND section, the bonds are correct: 5 2 3 ar 7 3 4 ar It seems anyway a good solution to change the script such that it checks the atom type when the atom id is ambiguous. I will work on it and see whether I can find a solution. Best wishes, Carmen ________________________________ From: autodock-bounces at scripps.edu on behalf of Van Dam, Hubertus Sent: Friday, September 4, 2020 5:32:45 PM To: autodock at scripps.edu Subject: Re: ADL: prepare_ligand4.py converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion Hi Carmen, Sorry, I was looking at atoms 2, 3, and 4 in 3R1_pH74_netcharge.mol2. They are listed as: 2 C1 2.1330 -2.3280 0.5080 ca 1 UNK 0.502600 3 C2 1.3340 -1.2480 0.8230 ca 1 UNK -0.458600 4 C3 1.9460 -0.0180 0.9010 ca 1 UNK 0.698200 So the atom ids are fine (column 2) but the atom types are wrong (column 6). But you are right atom 9 as you stated: 9 CA 5.9540 0.3730 -0.1620 c3 1 UNK 0.174500 has the correct atom type but is erroneously converted into a Calcium atom. The observations of the both of us agree that the prepare_ligand4.py script determines the atom type from the atom id and incorrectly ignores the atom type. Fixing this problem by going by the atom type will break what the code does for atoms 2-4. However, in your examples it should be sufficient if the script checked the atom type when the atom id is ambiguous. Typical atom ids causing trouble are: CA CD CE CF (? I seem to remember this one but don't have an example for it right now) HO (occurs in Amber or Charmm , means Hydrogen attached to Oxygen, not Holmium) I think these are the most common troublemakers. Best wishes, Huub ----------------------------------------------------------------------------------------------------- Hubertus van Dam, 631-344-6020, hvandam at bnl.gov Brookhaven National Laboratory ?On 9/4/20, 10:38, "autodock-bounces at scripps.edu on behalf of Esposito Carmen" wrote: Hi, Thank you for your reply. In the mol2, the atom named CA has the correct type c3 (and also the 3D structure is correct). 9 CA 5.9540 0.3730 -0.1620 c3 1 UNK 0.174500 The problem occurs only when I do the format conversion. In the pdbqt: ATOM 18 CA UNK d 1 5.954 0.373 -0.162 0.00 0.00 0.174 Ca ...All other carbon atoms named C1, C2, C3... are correctly recognised. So far, I corrected this error manually by modifying the line above, i.e. adjust the spacing between 18 and CA and replace "Ca" with "Ca". ATOM 18 CA UNK d 1 5.954 0.373 -0.162 0.00 0.00 0.174 C Anyway, I generated the mol2 file using the antechamber program from AmberTools20. After docking, I need to run MD simulations and this is why I parametrise the molecules in the first step. In this way, I can also use the same partial charges for docking. Best wishes, Carmen ________________________________ From: autodock-bounces at scripps.edu on behalf of Van Dam, Hubertus Sent: Friday, September 4, 2020 3:38:01 PM To: autodock at scripps.edu Subject: Re: ADL: prepare_ligand4.py converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion Hi Carmen, Where did you get the mol2 files from? In MOL2 files (see: https://urldefense.com/v3/__http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf__;!!P4SdNyxKAPE!WFeaSGPsDp6rIP35Id41VTgGAH4PixH8zqZ3Q8gUvQHg3DFEMHBaNYTDBApG5Es$ ) the atom types are supposed to be SYBYL atom types. I guess the alpha-carbons should be sp3 carbons (in most cases?) which would be indicated with C.3 (see: https://urldefense.com/v3/__http://tccc.iesl.forth.gr/education/local/quantum/molecular_modeling/guide_documents/SYBYL_data_document.html__;!!P4SdNyxKAPE!WFeaSGPsDp6rIP35Id41VTgGAH4PixH8zqZ3Q8gUvQHg3DFEMHBaNYTDODoQzyQ$ ). The atom type ca is actually Calcium. So I think the script is converting the MOL2 files correctly as far as I can see, it is just that the MOL2 files don't specify the structure as it should. Best wishes, Huub ----------------------------------------------------------------------------------------------------- Hubertus van Dam, 631-344-6020, hvandam at bnl.gov Brookhaven National Laboratory On 9/4/20, 04:59, "autodock-bounces at scripps.edu on behalf of Esposito Carmen" wrote: Hi! I am using the python script prepare_ligand4.py to convert mol2 files to pdbqt (I generate the mol2 files containing partial charges using antechamber of AmberTools20). pythonsh prepare_ligand4.py -l file.mol2 -C -o file.pdbqt However, I noticed that when doing the format conversion carbon atoms with the atom type CA (in the mol2) are transformed into calcium atoms (Ca, in the pdbqt file). I attached here a couple of examples. Is it possible that this is a bug? Thank you very much for your help! Best regards, Carmen ________________________________________________ --- ADL: AutoDock List --- https://urldefense.com/v3/__http://autodock.scripps.edu/mailing_list__;!!P4SdNyxKAPE!WFeaSGPsDp6rIP35Id41VTgGAH4PixH8zqZ3Q8gUvQHg3DFEMHBaNYTD77H6UPM$ --- ________________________________________________ --- ADL: AutoDock List --- https://urldefense.com/v3/__http://autodock.scripps.edu/mailing_list__;!!P4SdNyxKAPE!WFeaSGPsDp6rIP35Id41VTgGAH4PixH8zqZ3Q8gUvQHg3DFEMHBaNYTD77H6UPM$ --- ________________________________________________ --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list --- From mihaly.mezei at mssm.edu Sat Sep 5 05:20:15 2020 From: mihaly.mezei at mssm.edu (Mezei, Mihaly) Date: Sat, 5 Sep 2020 12:20:15 +0000 Subject: ADL: prepare_ligand4.py converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion In-Reply-To: References: Message-ID: <25DB14BA-3092-404B-8908-48227D8122A9@mssm.edu> Hello, the key to the puzzle is the PDB atom name convention that the first two characters of the name is the chemical symbol. Thus, making CA into calcium is not a bug. However, not all programs recognize this - hence the confusion. Mihaly Mezei Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai Voice: (212) 659-5475. Fax: (212) 849-2456 WWW (MSSM home): http://icahn.mssm.edu/profiles/mihaly-mezei WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei > On Sep 4, 2020, at 11:34 AM, Van Dam, Hubertus wrote: > > USE CAUTION: External Message. > > Hi Carmen, > > Sorry, I was looking at atoms 2, 3, and 4 in 3R1_pH74_netcharge.mol2. They are listed as: > > 2 C1 2.1330 -2.3280 0.5080 ca 1 UNK 0.502600 > 3 C2 1.3340 -1.2480 0.8230 ca 1 UNK -0.458600 > 4 C3 1.9460 -0.0180 0.9010 ca 1 UNK 0.698200 > > So the atom ids are fine (column 2) but the atom types are wrong (column 6). But you are right atom 9 as you stated: > > 9 CA 5.9540 0.3730 -0.1620 c3 1 UNK 0.174500 > > has the correct atom type but is erroneously converted into a Calcium atom. The observations of the both of us agree that the > > https://urldefense.proofpoint.com/v2/url?u=http-3A__prepare-5Fligand4.py&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=toBG7uPOawPYNuEr81UCajlWgtB_Qn6ymxLbJoFuTfk&s=yswljxPS786oN5qcesr7ZLVN13t7e593Dk1E50vwIDM&e= > > script determines the atom type from the atom id and incorrectly ignores the atom type. > > Fixing this problem by going by the atom type will break what the code does for atoms 2-4. However, in your examples it should be sufficient if the script checked the atom type when the atom id is ambiguous. Typical atom ids causing trouble are: > > CA > CD > CE > CF (? I seem to remember this one but don't have an example for it right now) > HO (occurs in Amber or Charmm , means Hydrogen attached to Oxygen, not Holmium) > > I think these are the most common troublemakers. > > Best wishes, > > Huub > > ----------------------------------------------------------------------------------------------------- > Hubertus van Dam, 631-344-6020, hvandam at bnl.gov > Brookhaven National Laboratory > > > ?On 9/4/20, 10:38, "autodock-bounces at scripps.edu on behalf of Esposito Carmen" wrote: > > Hi, > > > Thank you for your reply. > > In the mol2, the atom named CA has the correct type c3 (and also the 3D structure is correct). > > > 9 CA 5.9540 0.3730 -0.1620 c3 1 UNK 0.174500 > > > The problem occurs only when I do the format conversion. In the pdbqt: > > > ATOM 18 CA UNK d 1 5.954 0.373 -0.162 0.00 0.00 0.174 Ca > > > ...All other carbon atoms named C1, C2, C3... are correctly recognised. > > So far, I corrected this error manually by modifying the line above, i.e. adjust the spacing between 18 and CA and replace "Ca" with "Ca". > > > ATOM 18 CA UNK d 1 5.954 0.373 -0.162 0.00 0.00 0.174 C > > > Anyway, I generated the mol2 file using the antechamber program from AmberTools20. After docking, I need to run MD simulations and this is why I parametrise the molecules in the first step. In this way, I can also use the same partial charges for docking. > > > Best wishes, > > Carmen > > ________________________________ > From: autodock-bounces at scripps.edu on behalf of Van Dam, Hubertus > Sent: Friday, September 4, 2020 3:38:01 PM > To: autodock at scripps.edu > Subject: Re: ADL: https://urldefense.proofpoint.com/v2/url?u=http-3A__prepare-5Fligand4.py&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=toBG7uPOawPYNuEr81UCajlWgtB_Qn6ymxLbJoFuTfk&s=yswljxPS786oN5qcesr7ZLVN13t7e593Dk1E50vwIDM&e= converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion > > Hi Carmen, > > Where did you get the mol2 files from? In MOL2 files (see: https://urldefense.com/v3/__http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf__;!!P4SdNyxKAPE!WFeaSGPsDp6rIP35Id41VTgGAH4PixH8zqZ3Q8gUvQHg3DFEMHBaNYTDBApG5Es$ ) the atom types are supposed to be SYBYL atom types. I guess the alpha-carbons should be sp3 carbons (in most cases?) which would be indicated with C.3 (see: https://urldefense.com/v3/__http://tccc.iesl.forth.gr/education/local/quantum/molecular_modeling/guide_documents/SYBYL_data_document.html__;!!P4SdNyxKAPE!WFeaSGPsDp6rIP35Id41VTgGAH4PixH8zqZ3Q8gUvQHg3DFEMHBaNYTDODoQzyQ$ ). The atom type ca is actually Calcium. So I think the script is converting the MOL2 files correctly as far as I can see, it is just that the MOL2 files don't specify the structure as it should. > > Best wishes, > > Huub > > ----------------------------------------------------------------------------------------------------- > Hubertus van Dam, 631-344-6020, hvandam at bnl.gov > Brookhaven National Laboratory > > > On 9/4/20, 04:59, "autodock-bounces at scripps.edu on behalf of Esposito Carmen" wrote: > > Hi! > > I am using the python script https://urldefense.proofpoint.com/v2/url?u=http-3A__prepare-5Fligand4.py&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=toBG7uPOawPYNuEr81UCajlWgtB_Qn6ymxLbJoFuTfk&s=yswljxPS786oN5qcesr7ZLVN13t7e593Dk1E50vwIDM&e= to convert mol2 files to pdbqt (I generate the mol2 files containing partial charges using antechamber of AmberTools20). > > pythonsh https://urldefense.proofpoint.com/v2/url?u=http-3A__prepare-5Fligand4.py&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=toBG7uPOawPYNuEr81UCajlWgtB_Qn6ymxLbJoFuTfk&s=yswljxPS786oN5qcesr7ZLVN13t7e593Dk1E50vwIDM&e= -l file.mol2 -C -o file.pdbqt > > However, I noticed that when doing the format conversion carbon atoms with the atom type CA (in the mol2) are transformed into calcium atoms (Ca, in the pdbqt file). > I attached here a couple of examples. > Is it possible that this is a bug? > > Thank you very much for your help! > > Best regards, > Carmen > > > > ________________________________________________ > --- ADL: AutoDock List --- https://urldefense.com/v3/__http://autodock.scripps.edu/mailing_list__;!!P4SdNyxKAPE!WFeaSGPsDp6rIP35Id41VTgGAH4PixH8zqZ3Q8gUvQHg3DFEMHBaNYTD77H6UPM$ --- > ________________________________________________ > --- ADL: AutoDock List --- https://urldefense.com/v3/__http://autodock.scripps.edu/mailing_list__;!!P4SdNyxKAPE!WFeaSGPsDp6rIP35Id41VTgGAH4PixH8zqZ3Q8gUvQHg3DFEMHBaNYTD77H6UPM$ --- > > > ________________________________________________ > --- ADL: AutoDock List --- https://urldefense.proofpoint.com/v2/url?u=http-3A__autodock.scripps.edu_mailing-5Flist&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=toBG7uPOawPYNuEr81UCajlWgtB_Qn6ymxLbJoFuTfk&s=8Abj2-PSBDbiuFPOWn63NeX-aCNEAtP2kiNDxGhqjkM&e= --- From sherif.elsabbagh at hotmail.com Sat Sep 5 14:53:51 2020 From: sherif.elsabbagh at hotmail.com (Sherif Arafa) Date: Sat, 5 Sep 2020 21:53:51 +0000 Subject: ADL: Mgltools not working on mac Message-ID: Hi I have mac OS catalina and the MGL Tools can not open. Is there any news about other way to use it Sherif Elsabbagh PhD Candidate Institute of Pharmacy University of Tuebingen 72076, Heuberger Tor Weg 15, Tuebingen From hvandam at bnl.gov Sat Sep 5 15:21:20 2020 From: hvandam at bnl.gov (Van Dam, Hubertus) Date: Sat, 5 Sep 2020 22:21:20 +0000 Subject: ADL: Mgltools not working on mac In-Reply-To: References: Message-ID: <92E8E823-9ED8-4906-815A-BB09FB3CC7C4@bnl.gov> HI Sherif, The current advice is to install VirtualBox and run the Linux version of MGLTools inside it (https://ccsb.scripps.edu/mgltools/). VirtualBox is a virtual machine (VM) that allows you to install any OS within it and build your own environment in terms of packages. Best wishes, Huub ----------------------------------------------------------------------------------------------------- Hubertus van Dam, 631-344-6020, hvandam at bnl.gov Brookhaven National Laboratory ?On 9/5/20, 17:57, "autodock-bounces at scripps.edu on behalf of Sherif Arafa" wrote: Hi I have mac OS catalina and the MGL Tools can not open. Is there any news about other way to use it Sherif Elsabbagh PhD Candidate Institute of Pharmacy University of Tuebingen 72076, Heuberger Tor Weg 15, Tuebingen ________________________________________________ --- ADL: AutoDock List --- https://urldefense.com/v3/__http://autodock.scripps.edu/mailing_list__;!!P4SdNyxKAPE!Q-awqmD9wxLBEx388TLo7B_Al3UiCcM6H9sAyMcNTNu4VscJQsDwyBNdJtAkYG4$ --- From hvandam at bnl.gov Sat Sep 5 17:11:16 2020 From: hvandam at bnl.gov (Van Dam, Hubertus) Date: Sun, 6 Sep 2020 00:11:16 +0000 Subject: ADL: prepare_ligand4.py converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion Message-ID: <7985A428-7AEE-41BE-B114-A40B19DDBEEF@bnl.gov> Hi Mihaly, I am sorry but I don't think your statement is entirely correct. In PDB files how atom names are to be interpreted depends on the position in the line (see: https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM) as well as the atom name. I.e. "CA" in columns 13 and 14 is Calcium, "CA" in columns 14 and 15 is an alpha-Carbon. The other issue is that the files discussed here are MOL2 files. How the atom names in MOL2 files are to be interpreted does not have to be the same as that in PDB files. In fact a "calcium" atom with the atom type "sp3-hybridized Carbon" does not make any sense. The document that describes the MOL2 format (see: http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf page 12) actually gives an alpha-Carbon as an example, suggesting that the MOL2 format allows using the PDB atom names but that the atom type has to resolve ambiguous atom names (i.e. atom_name=CA and atom_type=ca is Calcium, whereas atom_name=CA and atom_type=c.3 is an alpha-Carbon). Admittedly the MOL2 document is not very explicit about how atom names are to be interpreted, which might be a major source of confusion. Best wishes, Huub ----------------------------------------------------------------------------------------------------- Hubertus van Dam, 631-344-6020, hvandam at bnl.gov Brookhaven National Laboratory ?On 9/5/20, 08:23, "autodock-bounces at scripps.edu on behalf of Mezei, Mihaly" wrote: Hello, the key to the puzzle is the PDB atom name convention that the first two characters of the name is the chemical symbol. Thus, making CA into calcium is not a bug. However, not all programs recognize this - hence the confusion. Mihaly Mezei Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai Voice: (212) 659-5475. Fax: (212) 849-2456 WWW (MSSM home): https://urldefense.com/v3/__http://icahn.mssm.edu/profiles/mihaly-mezei__;!!P4SdNyxKAPE!WEn3f8DCbnLnbWtO2vxZMl9b16m5WCGAlsv6mmiEdISSpkSIQC8zl2IYFX9HOO8$ WWW (Lab home - software, publications): https://urldefense.com/v3/__http://inka.mssm.edu/*mezei__;fg!!P4SdNyxKAPE!WEn3f8DCbnLnbWtO2vxZMl9b16m5WCGAlsv6mmiEdISSpkSIQC8zl2IYqc7b-EU$ > On Sep 4, 2020, at 11:34 AM, Van Dam, Hubertus wrote: > > USE CAUTION: External Message. > > Hi Carmen, > > Sorry, I was looking at atoms 2, 3, and 4 in 3R1_pH74_netcharge.mol2. They are listed as: > > 2 C1 2.1330 -2.3280 0.5080 ca 1 UNK 0.502600 > 3 C2 1.3340 -1.2480 0.8230 ca 1 UNK -0.458600 > 4 C3 1.9460 -0.0180 0.9010 ca 1 UNK 0.698200 > > So the atom ids are fine (column 2) but the atom types are wrong (column 6). But you are right atom 9 as you stated: > > 9 CA 5.9540 0.3730 -0.1620 c3 1 UNK 0.174500 > > has the correct atom type but is erroneously converted into a Calcium atom. The observations of the both of us agree that the > > https://urldefense.proofpoint.com/v2/url?u=http-3A__prepare-5Fligand4.py&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=toBG7uPOawPYNuEr81UCajlWgtB_Qn6ymxLbJoFuTfk&s=yswljxPS786oN5qcesr7ZLVN13t7e593Dk1E50vwIDM&e= > > script determines the atom type from the atom id and incorrectly ignores the atom type. > > Fixing this problem by going by the atom type will break what the code does for atoms 2-4. However, in your examples it should be sufficient if the script checked the atom type when the atom id is ambiguous. Typical atom ids causing trouble are: > > CA > CD > CE > CF (? I seem to remember this one but don't have an example for it right now) > HO (occurs in Amber or Charmm , means Hydrogen attached to Oxygen, not Holmium) > > I think these are the most common troublemakers. > > Best wishes, > > Huub > > ----------------------------------------------------------------------------------------------------- > Hubertus van Dam, 631-344-6020, hvandam at bnl.gov > Brookhaven National Laboratory > > > On 9/4/20, 10:38, "autodock-bounces at scripps.edu on behalf of Esposito Carmen" wrote: > > Hi, > > > Thank you for your reply. > > In the mol2, the atom named CA has the correct type c3 (and also the 3D structure is correct). > > > 9 CA 5.9540 0.3730 -0.1620 c3 1 UNK 0.174500 > > > The problem occurs only when I do the format conversion. In the pdbqt: > > > ATOM 18 CA UNK d 1 5.954 0.373 -0.162 0.00 0.00 0.174 Ca > > > ...All other carbon atoms named C1, C2, C3... are correctly recognised. > > So far, I corrected this error manually by modifying the line above, i.e. adjust the spacing between 18 and CA and replace "Ca" with "Ca". > > > ATOM 18 CA UNK d 1 5.954 0.373 -0.162 0.00 0.00 0.174 C > > > Anyway, I generated the mol2 file using the antechamber program from AmberTools20. After docking, I need to run MD simulations and this is why I parametrise the molecules in the first step. In this way, I can also use the same partial charges for docking. > > > Best wishes, > > Carmen > > ________________________________ > From: autodock-bounces at scripps.edu on behalf of Van Dam, Hubertus > Sent: Friday, September 4, 2020 3:38:01 PM > To: autodock at scripps.edu > Subject: Re: ADL: https://urldefense.proofpoint.com/v2/url?u=http-3A__prepare-5Fligand4.py&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=toBG7uPOawPYNuEr81UCajlWgtB_Qn6ymxLbJoFuTfk&s=yswljxPS786oN5qcesr7ZLVN13t7e593Dk1E50vwIDM&e= converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion > > Hi Carmen, > > Where did you get the mol2 files from? In MOL2 files (see: https://urldefense.com/v3/__http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf__;!!P4SdNyxKAPE!WFeaSGPsDp6rIP35Id41VTgGAH4PixH8zqZ3Q8gUvQHg3DFEMHBaNYTDBApG5Es$ ) the atom types are supposed to be SYBYL atom types. I guess the alpha-carbons should be sp3 carbons (in most cases?) which would be indicated with C.3 (see: https://urldefense.com/v3/__http://tccc.iesl.forth.gr/education/local/quantum/molecular_modeling/guide_documents/SYBYL_data_document.html__;!!P4SdNyxKAPE!WFeaSGPsDp6rIP35Id41VTgGAH4PixH8zqZ3Q8gUvQHg3DFEMHBaNYTDODoQzyQ$ ). The atom type ca is actually Calcium. So I think the script is converting the MOL2 files correctly as far as I can see, it is just that the MOL2 files don't specify the structure as it should. > > Best wishes, > > Huub > > ----------------------------------------------------------------------------------------------------- > Hubertus van Dam, 631-344-6020, hvandam at bnl.gov > Brookhaven National Laboratory > > > On 9/4/20, 04:59, "autodock-bounces at scripps.edu on behalf of Esposito Carmen" wrote: > > Hi! > > I am using the python script https://urldefense.proofpoint.com/v2/url?u=http-3A__prepare-5Fligand4.py&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=toBG7uPOawPYNuEr81UCajlWgtB_Qn6ymxLbJoFuTfk&s=yswljxPS786oN5qcesr7ZLVN13t7e593Dk1E50vwIDM&e= to convert mol2 files to pdbqt (I generate the mol2 files containing partial charges using antechamber of AmberTools20). > > pythonsh https://urldefense.proofpoint.com/v2/url?u=http-3A__prepare-5Fligand4.py&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=toBG7uPOawPYNuEr81UCajlWgtB_Qn6ymxLbJoFuTfk&s=yswljxPS786oN5qcesr7ZLVN13t7e593Dk1E50vwIDM&e= -l file.mol2 -C -o file.pdbqt > > However, I noticed that when doing the format conversion carbon atoms with the atom type CA (in the mol2) are transformed into calcium atoms (Ca, in the pdbqt file). > I attached here a couple of examples. > Is it possible that this is a bug? > > Thank you very much for your help! > > Best regards, > Carmen > > > > ________________________________________________ > --- ADL: AutoDock List --- https://urldefense.com/v3/__http://autodock.scripps.edu/mailing_list__;!!P4SdNyxKAPE!WFeaSGPsDp6rIP35Id41VTgGAH4PixH8zqZ3Q8gUvQHg3DFEMHBaNYTD77H6UPM$ --- > ________________________________________________ > --- ADL: AutoDock List --- https://urldefense.com/v3/__http://autodock.scripps.edu/mailing_list__;!!P4SdNyxKAPE!WFeaSGPsDp6rIP35Id41VTgGAH4PixH8zqZ3Q8gUvQHg3DFEMHBaNYTD77H6UPM$ --- > > > ________________________________________________ > --- ADL: AutoDock List --- https://urldefense.proofpoint.com/v2/url?u=http-3A__autodock.scripps.edu_mailing-5Flist&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=toBG7uPOawPYNuEr81UCajlWgtB_Qn6ymxLbJoFuTfk&s=8Abj2-PSBDbiuFPOWn63NeX-aCNEAtP2kiNDxGhqjkM&e= --- ________________________________________________ --- ADL: AutoDock List --- https://urldefense.com/v3/__http://autodock.scripps.edu/mailing_list__;!!P4SdNyxKAPE!WEn3f8DCbnLnbWtO2vxZMl9b16m5WCGAlsv6mmiEdISSpkSIQC8zl2IYJ-Fn6Is$ --- From jpfarrell at uchicago.edu Tue Sep 8 19:33:40 2020 From: jpfarrell at uchicago.edu (Joey Farrell) Date: Wed, 9 Sep 2020 02:33:40 +0000 Subject: ADL: Protonating Macromolecule / Docking at Different pH Message-ID: Hi all, I was wondering if there are any recommendations as to how to go about running a docking simulation using AutoDockTools and Autodock Vina at various pH levels. One potentially useful resource I found was H++, which evidently has automated pK calculation and corresponding charging/protonation, but I am not sure if there are other tools better suited for the task. Furthermore, in this case, should the application of Kollman/Gasteiger charges be skipped? I would appreciate any insight on running docking simulations using this suite of tools at different pH levels. Thank you in advance! Best, Joey From josh at rosabio.tech Wed Sep 9 03:25:12 2020 From: josh at rosabio.tech (josh at rosabio.tech) Date: Wed, 9 Sep 2020 11:25:12 +0100 Subject: ADL: Grid box spacing in Vina Message-ID: Hey guys, Apologies if this has been asked before. I am playing around with different Grid Box sizes, total grid points and exhaustiveness parameters in Vina, trying to get the largest search space for my systems without incurring excessively long runs. I am wondering, what influence does ?total grid points per map? have on a Vina run? I believe I read somewhere that the spacing term is more important for Autodock4 rather than Vina. I have tried increasing the size of my Grid Box by increasing spacing to 1 A, and thus producing a larger grid box for a lower ?Grid Points Per Map? term ? but I am not sure it is that influential in the length of my runs ? can anyone advise on this? Many thanks, Josh From carmen.esposito at phys.chem.ethz.ch Wed Sep 9 03:59:54 2020 From: carmen.esposito at phys.chem.ethz.ch (Esposito Carmen) Date: Wed, 9 Sep 2020 10:59:54 +0000 Subject: ADL: prepare_ligand4.py converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion In-Reply-To: <7985A428-7AEE-41BE-B114-A40B19DDBEEF@bnl.gov> References: <7985A428-7AEE-41BE-B114-A40B19DDBEEF@bnl.gov> Message-ID: <0da18666bacc458faeb678c17b595a3b@phys.chem.ethz.ch> Hi Mihaly, Hi Huub, I agree with the comment of Huub. In addition, I want to use the mol2 file because it has the charges generated using antechamber and I want to use these charges for the docking. Anyway... I found that atoms named "CA" are defined as calcium atoms in the AutoDockTools parameter files AD4.1_bound.dat and AD4_parameters.dat. atom_par Ca 1.98 0.550 2.7700 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding Calcium atom_par CA 1.98 0.550 2.7700 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding Calcium However, I did not find yet how to solve this issue such that the prepare_ligand4.py script relies on the atom types, e.g. c3, and not on the atom names to identify elements. The easiest solution is to rename the the "CA" carbon atoms as, e.g., "C99", in the mol2 file before running the prepare_ligand4.py script ( I assume that small molecules usually have less than 100 carbon atoms; hence the "C99" atom name is unique). sed -i 's/ CA / C99/g' file.mol2 Best wishes, Carmen ________________________________ From: autodock-bounces at scripps.edu on behalf of Van Dam, Hubertus Sent: Sunday, September 6, 2020 2:11:16 AM To: autodock at scripps.edu Subject: Re: ADL: prepare_ligand4.py converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion Hi Mihaly, I am sorry but I don't think your statement is entirely correct. In PDB files how atom names are to be interpreted depends on the position in the line (see: https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM) as well as the atom name. I.e. "CA" in columns 13 and 14 is Calcium, "CA" in columns 14 and 15 is an alpha-Carbon. The other issue is that the files discussed here are MOL2 files. How the atom names in MOL2 files are to be interpreted does not have to be the same as that in PDB files. In fact a "calcium" atom with the atom type "sp3-hybridized Carbon" does not make any sense. The document that describes the MOL2 format (see: http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf page 12) actually gives an alpha-Carbon as an example, suggesting that the MOL2 format allows using the PDB atom names but that the atom type has to resolve ambiguous atom names (i.e. atom_name=CA and atom_type=ca is Calcium, whereas atom_name=CA and atom_type=c.3 is an alpha-Carbon). Admittedly the MOL2 document is not very explicit about how atom names are to be interpreted, which might be a major source of confusion. Best wishes, Huub ----------------------------------------------------------------------------------------------------- Hubertus van Dam, 631-344-6020, hvandam at bnl.gov Brookhaven National Laboratory ?On 9/5/20, 08:23, "autodock-bounces at scripps.edu on behalf of Mezei, Mihaly" wrote: Hello, the key to the puzzle is the PDB atom name convention that the first two characters of the name is the chemical symbol. Thus, making CA into calcium is not a bug. However, not all programs recognize this - hence the confusion. Mihaly Mezei Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai Voice: (212) 659-5475. Fax: (212) 849-2456 WWW (MSSM home): https://urldefense.com/v3/__http://icahn.mssm.edu/profiles/mihaly-mezei__;!!P4SdNyxKAPE!WEn3f8DCbnLnbWtO2vxZMl9b16m5WCGAlsv6mmiEdISSpkSIQC8zl2IYFX9HOO8$ WWW (Lab home - software, publications): https://urldefense.com/v3/__http://inka.mssm.edu/*mezei__;fg!!P4SdNyxKAPE!WEn3f8DCbnLnbWtO2vxZMl9b16m5WCGAlsv6mmiEdISSpkSIQC8zl2IYqc7b-EU$ > On Sep 4, 2020, at 11:34 AM, Van Dam, Hubertus wrote: > > USE CAUTION: External Message. > > Hi Carmen, > > Sorry, I was looking at atoms 2, 3, and 4 in 3R1_pH74_netcharge.mol2. They are listed as: > > 2 C1 2.1330 -2.3280 0.5080 ca 1 UNK 0.502600 > 3 C2 1.3340 -1.2480 0.8230 ca 1 UNK -0.458600 > 4 C3 1.9460 -0.0180 0.9010 ca 1 UNK 0.698200 > > So the atom ids are fine (column 2) but the atom types are wrong (column 6). But you are right atom 9 as you stated: > > 9 CA 5.9540 0.3730 -0.1620 c3 1 UNK 0.174500 > > has the correct atom type but is erroneously converted into a Calcium atom. The observations of the both of us agree that the > > https://urldefense.proofpoint.com/v2/url?u=http-3A__prepare-5Fligand4.py&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=toBG7uPOawPYNuEr81UCajlWgtB_Qn6ymxLbJoFuTfk&s=yswljxPS786oN5qcesr7ZLVN13t7e593Dk1E50vwIDM&e= > > script determines the atom type from the atom id and incorrectly ignores the atom type. > > Fixing this problem by going by the atom type will break what the code does for atoms 2-4. However, in your examples it should be sufficient if the script checked the atom type when the atom id is ambiguous. Typical atom ids causing trouble are: > > CA > CD > CE > CF (? I seem to remember this one but don't have an example for it right now) > HO (occurs in Amber or Charmm , means Hydrogen attached to Oxygen, not Holmium) > > I think these are the most common troublemakers. > > Best wishes, > > Huub > > ----------------------------------------------------------------------------------------------------- > Hubertus van Dam, 631-344-6020, hvandam at bnl.gov > Brookhaven National Laboratory > > > On 9/4/20, 10:38, "autodock-bounces at scripps.edu on behalf of Esposito Carmen" wrote: > > Hi, > > > Thank you for your reply. > > In the mol2, the atom named CA has the correct type c3 (and also the 3D structure is correct). > > > 9 CA 5.9540 0.3730 -0.1620 c3 1 UNK 0.174500 > > > The problem occurs only when I do the format conversion. In the pdbqt: > > > ATOM 18 CA UNK d 1 5.954 0.373 -0.162 0.00 0.00 0.174 Ca > > > ...All other carbon atoms named C1, C2, C3... are correctly recognised. > > So far, I corrected this error manually by modifying the line above, i.e. adjust the spacing between 18 and CA and replace "Ca" with "Ca". > > > ATOM 18 CA UNK d 1 5.954 0.373 -0.162 0.00 0.00 0.174 C > > > Anyway, I generated the mol2 file using the antechamber program from AmberTools20. After docking, I need to run MD simulations and this is why I parametrise the molecules in the first step. In this way, I can also use the same partial charges for docking. > > > Best wishes, > > Carmen > > ________________________________ > From: autodock-bounces at scripps.edu on behalf of Van Dam, Hubertus > Sent: Friday, September 4, 2020 3:38:01 PM > To: autodock at scripps.edu > Subject: Re: ADL: https://urldefense.proofpoint.com/v2/url?u=http-3A__prepare-5Fligand4.py&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=toBG7uPOawPYNuEr81UCajlWgtB_Qn6ymxLbJoFuTfk&s=yswljxPS786oN5qcesr7ZLVN13t7e593Dk1E50vwIDM&e= converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion > > Hi Carmen, > > Where did you get the mol2 files from? In MOL2 files (see: https://urldefense.com/v3/__http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf__;!!P4SdNyxKAPE!WFeaSGPsDp6rIP35Id41VTgGAH4PixH8zqZ3Q8gUvQHg3DFEMHBaNYTDBApG5Es$ ) the atom types are supposed to be SYBYL atom types. I guess the alpha-carbons should be sp3 carbons (in most cases?) which would be indicated with C.3 (see: https://urldefense.com/v3/__http://tccc.iesl.forth.gr/education/local/quantum/molecular_modeling/guide_documents/SYBYL_data_document.html__;!!P4SdNyxKAPE!WFeaSGPsDp6rIP35Id41VTgGAH4PixH8zqZ3Q8gUvQHg3DFEMHBaNYTDODoQzyQ$ ). The atom type ca is actually Calcium. So I think the script is converting the MOL2 files correctly as far as I can see, it is just that the MOL2 files don't specify the structure as it should. > > Best wishes, > > Huub > > ----------------------------------------------------------------------------------------------------- > Hubertus van Dam, 631-344-6020, hvandam at bnl.gov > Brookhaven National Laboratory > > > On 9/4/20, 04:59, "autodock-bounces at scripps.edu on behalf of Esposito Carmen" wrote: > > Hi! > > I am using the python script https://urldefense.proofpoint.com/v2/url?u=http-3A__prepare-5Fligand4.py&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=toBG7uPOawPYNuEr81UCajlWgtB_Qn6ymxLbJoFuTfk&s=yswljxPS786oN5qcesr7ZLVN13t7e593Dk1E50vwIDM&e= to convert mol2 files to pdbqt (I generate the mol2 files containing partial charges using antechamber of AmberTools20). > > pythonsh https://urldefense.proofpoint.com/v2/url?u=http-3A__prepare-5Fligand4.py&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=toBG7uPOawPYNuEr81UCajlWgtB_Qn6ymxLbJoFuTfk&s=yswljxPS786oN5qcesr7ZLVN13t7e593Dk1E50vwIDM&e= -l file.mol2 -C -o file.pdbqt > > However, I noticed that when doing the format conversion carbon atoms with the atom type CA (in the mol2) are transformed into calcium atoms (Ca, in the pdbqt file). > I attached here a couple of examples. > Is it possible that this is a bug? > > Thank you very much for your help! > > Best regards, > Carmen > > > > ________________________________________________ > --- ADL: AutoDock List --- https://urldefense.com/v3/__http://autodock.scripps.edu/mailing_list__;!!P4SdNyxKAPE!WFeaSGPsDp6rIP35Id41VTgGAH4PixH8zqZ3Q8gUvQHg3DFEMHBaNYTD77H6UPM$ --- > ________________________________________________ > --- ADL: AutoDock List --- https://urldefense.com/v3/__http://autodock.scripps.edu/mailing_list__;!!P4SdNyxKAPE!WFeaSGPsDp6rIP35Id41VTgGAH4PixH8zqZ3Q8gUvQHg3DFEMHBaNYTD77H6UPM$ --- > > > ________________________________________________ > --- ADL: AutoDock List --- https://urldefense.proofpoint.com/v2/url?u=http-3A__autodock.scripps.edu_mailing-5Flist&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=toBG7uPOawPYNuEr81UCajlWgtB_Qn6ymxLbJoFuTfk&s=8Abj2-PSBDbiuFPOWn63NeX-aCNEAtP2kiNDxGhqjkM&e= --- ________________________________________________ --- ADL: AutoDock List --- https://urldefense.com/v3/__http://autodock.scripps.edu/mailing_list__;!!P4SdNyxKAPE!WEn3f8DCbnLnbWtO2vxZMl9b16m5WCGAlsv6mmiEdISSpkSIQC8zl2IYJ-Fn6Is$ --- ________________________________________________ --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list --- From diogo.stmart at gmail.com Wed Sep 9 08:53:09 2020 From: diogo.stmart at gmail.com (Diogo Martins) Date: Wed, 9 Sep 2020 08:53:09 -0700 Subject: ADL: Grid box spacing in Vina In-Reply-To: References: Message-ID: Hi Josh, The spacing in Vina is hard-coded to 0.375 angstrom. The only way to change the spacing is to edit the source code and recompile Vina. The size of the box does not affect the number of monte carlo steps, so the runtime won't change much, but it will take a little longer to calculate a larger box. It may be a good idea to increase "--exhaustiveness" if the box is too large. Hope this helps, On Wed, 9 Sep 2020 at 03:26, wrote: > > Hey guys, > > > Apologies if this has been asked before. I am playing around with > different > Grid Box sizes, total grid points and exhaustiveness parameters in Vina, > trying to get the largest search space for my systems without incurring > excessively long runs. I am wondering, what influence does ?total grid > points per map? have on a Vina run? I believe I read somewhere that the > spacing term is more important for Autodock4 rather than Vina. > > > I have tried increasing the size of my Grid Box by increasing spacing > to 1 > A, and thus producing a larger grid box for a lower ?Grid Points Per > Map? > term ? but I am not sure it is that influential in the length of my > runs ? > can anyone advise on this? > > > Many thanks, > > > Josh > ________________________________________________ > --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list --- From hvandam at bnl.gov Wed Sep 9 10:01:45 2020 From: hvandam at bnl.gov (Van Dam, Hubertus) Date: Wed, 9 Sep 2020 17:01:45 +0000 Subject: ADL: prepare_ligand4.py converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion Message-ID: <5433B249-55D4-41A6-94DA-C25CE864C55E@bnl.gov> Hi Carmen, I think the underlying problem is likely to be that Amber uses a MOL2 dialect. It would seem that Amber uses the atom type "ca" to select a particular set of force field parameters for Carbon atoms that are not covered by any of the other MOL2 atom types. There is enough information in the atom names and the atom types to resolve this as long as the atom names correspond to the PDB atom names. As long as that is the case it is possible to write a Tripos MOL2 to Amber MOL2 converter and vice versa without losing information so that you could actually convert either MOL2 file back to PDB. The question is where such a tool should live. I guess the best place for it to go would be the Amber Tools. However, I don't know if they accept contributed utilities, I will ask. Best wishes, Huub ----------------------------------------------------------------------------------------------------- Hubertus van Dam, 631-344-6020, hvandam at bnl.gov Brookhaven National Laboratory ?On 9/9/20, 07:01, "autodock-bounces at scripps.edu on behalf of Esposito Carmen" wrote: Hi Mihaly, Hi Huub, I agree with the comment of Huub. In addition, I want to use the mol2 file because it has the charges generated using antechamber and I want to use these charges for the docking. Anyway... I found that atoms named "CA" are defined as calcium atoms in the AutoDockTools parameter files AD4.1_bound.dat and AD4_parameters.dat. atom_par Ca 1.98 0.550 2.7700 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding Calcium atom_par CA 1.98 0.550 2.7700 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding Calcium However, I did not find yet how to solve this issue such that the prepare_ligand4.py script relies on the atom types, e.g. c3, and not on the atom names to identify elements. The easiest solution is to rename the the "CA" carbon atoms as, e.g., "C99", in the mol2 file before running the prepare_ligand4.py script ( I assume that small molecules usually have less than 100 carbon atoms; hence the "C99" atom name is unique). sed -i 's/ CA / C99/g' file.mol2 Best wishes, Carmen ________________________________ From: autodock-bounces at scripps.edu on behalf of Van Dam, Hubertus Sent: Sunday, September 6, 2020 2:11:16 AM To: autodock at scripps.edu Subject: Re: ADL: prepare_ligand4.py converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion Hi Mihaly, I am sorry but I don't think your statement is entirely correct. In PDB files how atom names are to be interpreted depends on the position in the line (see: https://urldefense.com/v3/__https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html*ATOM__;Iw!!P4SdNyxKAPE!TkhOlZfuqX8ODbmxzZ23CqWJHAbdj0KSQUaJWoW8lG6PNCeTljQorrWMGeNuImc$ ) as well as the atom name. I.e. "CA" in columns 13 and 14 is Calcium, "CA" in columns 14 and 15 is an alpha-Carbon. The other issue is that the files discussed here are MOL2 files. How the atom names in MOL2 files are to be interpreted does not have to be the same as that in PDB files. In fact a "calcium" atom with the atom type "sp3-hybridized Carbon" does not make any sense. The document that describes the MOL2 format (see: https://urldefense.com/v3/__http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf__;!!P4SdNyxKAPE!TkhOlZfuqX8ODbmxzZ23CqWJHAbdj0KSQUaJWoW8lG6PNCeTljQorrWMceE5X2I$ page 12) actually gives an alpha-Carbon as an example, suggesting that the MOL2 format allows using the PDB atom names but that the atom type has to resolve ambiguous atom names (i.e. atom_name=CA and atom_type=ca is Calcium, whereas atom_name=CA and atom_type=c.3 is an alpha-Carbon). Admittedly the MOL2 document is not very explicit about how atom names are to be interpreted, which might be a major source of confusion. Best wishes, Huub ----------------------------------------------------------------------------------------------------- Hubertus van Dam, 631-344-6020, hvandam at bnl.gov Brookhaven National Laboratory On 9/5/20, 08:23, "autodock-bounces at scripps.edu on behalf of Mezei, Mihaly" wrote: Hello, the key to the puzzle is the PDB atom name convention that the first two characters of the name is the chemical symbol. Thus, making CA into calcium is not a bug. However, not all programs recognize this - hence the confusion. Mihaly Mezei Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai Voice: (212) 659-5475. Fax: (212) 849-2456 WWW (MSSM home): https://urldefense.com/v3/__http://icahn.mssm.edu/profiles/mihaly-mezei__;!!P4SdNyxKAPE!WEn3f8DCbnLnbWtO2vxZMl9b16m5WCGAlsv6mmiEdISSpkSIQC8zl2IYFX9HOO8$ WWW (Lab home - software, publications): https://urldefense.com/v3/__http://inka.mssm.edu/*mezei__;fg!!P4SdNyxKAPE!WEn3f8DCbnLnbWtO2vxZMl9b16m5WCGAlsv6mmiEdISSpkSIQC8zl2IYqc7b-EU$ > On Sep 4, 2020, at 11:34 AM, Van Dam, Hubertus wrote: > > USE CAUTION: External Message. > > Hi Carmen, > > Sorry, I was looking at atoms 2, 3, and 4 in 3R1_pH74_netcharge.mol2. They are listed as: > > 2 C1 2.1330 -2.3280 0.5080 ca 1 UNK 0.502600 > 3 C2 1.3340 -1.2480 0.8230 ca 1 UNK -0.458600 > 4 C3 1.9460 -0.0180 0.9010 ca 1 UNK 0.698200 > > So the atom ids are fine (column 2) but the atom types are wrong (column 6). But you are right atom 9 as you stated: > > 9 CA 5.9540 0.3730 -0.1620 c3 1 UNK 0.174500 > > has the correct atom type but is erroneously converted into a Calcium atom. The observations of the both of us agree that the > > https://urldefense.proofpoint.com/v2/url?u=http-3A__prepare-5Fligand4.py&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=toBG7uPOawPYNuEr81UCajlWgtB_Qn6ymxLbJoFuTfk&s=yswljxPS786oN5qcesr7ZLVN13t7e593Dk1E50vwIDM&e= > > script determines the atom type from the atom id and incorrectly ignores the atom type. > > Fixing this problem by going by the atom type will break what the code does for atoms 2-4. However, in your examples it should be sufficient if the script checked the atom type when the atom id is ambiguous. Typical atom ids causing trouble are: > > CA > CD > CE > CF (? I seem to remember this one but don't have an example for it right now) > HO (occurs in Amber or Charmm , means Hydrogen attached to Oxygen, not Holmium) > > I think these are the most common troublemakers. > > Best wishes, > > Huub > > ----------------------------------------------------------------------------------------------------- > Hubertus van Dam, 631-344-6020, hvandam at bnl.gov > Brookhaven National Laboratory > > > On 9/4/20, 10:38, "autodock-bounces at scripps.edu on behalf of Esposito Carmen" wrote: > > Hi, > > > Thank you for your reply. > > In the mol2, the atom named CA has the correct type c3 (and also the 3D structure is correct). > > > 9 CA 5.9540 0.3730 -0.1620 c3 1 UNK 0.174500 > > > The problem occurs only when I do the format conversion. In the pdbqt: > > > ATOM 18 CA UNK d 1 5.954 0.373 -0.162 0.00 0.00 0.174 Ca > > > ...All other carbon atoms named C1, C2, C3... are correctly recognised. > > So far, I corrected this error manually by modifying the line above, i.e. adjust the spacing between 18 and CA and replace "Ca" with "Ca". > > > ATOM 18 CA UNK d 1 5.954 0.373 -0.162 0.00 0.00 0.174 C > > > Anyway, I generated the mol2 file using the antechamber program from AmberTools20. After docking, I need to run MD simulations and this is why I parametrise the molecules in the first step. In this way, I can also use the same partial charges for docking. > > > Best wishes, > > Carmen > > ________________________________ > From: autodock-bounces at scripps.edu on behalf of Van Dam, Hubertus > Sent: Friday, September 4, 2020 3:38:01 PM > To: autodock at scripps.edu > Subject: Re: ADL: https://urldefense.proofpoint.com/v2/url?u=http-3A__prepare-5Fligand4.py&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=toBG7uPOawPYNuEr81UCajlWgtB_Qn6ymxLbJoFuTfk&s=yswljxPS786oN5qcesr7ZLVN13t7e593Dk1E50vwIDM&e= converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion > > Hi Carmen, > > Where did you get the mol2 files from? In MOL2 files (see: https://urldefense.com/v3/__http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf__;!!P4SdNyxKAPE!WFeaSGPsDp6rIP35Id41VTgGAH4PixH8zqZ3Q8gUvQHg3DFEMHBaNYTDBApG5Es$ ) the atom types are supposed to be SYBYL atom types. I guess the alpha-carbons should be sp3 carbons (in most cases?) which would be indicated with C.3 (see: https://urldefense.com/v3/__http://tccc.iesl.forth.gr/education/local/quantum/molecular_modeling/guide_documents/SYBYL_data_document.html__;!!P4SdNyxKAPE!WFeaSGPsDp6rIP35Id41VTgGAH4PixH8zqZ3Q8gUvQHg3DFEMHBaNYTDODoQzyQ$ ). The atom type ca is actually Calcium. So I think the script is converting the MOL2 files correctly as far as I can see, it is just that the MOL2 files don't specify the structure as it should. > > Best wishes, > > Huub > > ----------------------------------------------------------------------------------------------------- > Hubertus van Dam, 631-344-6020, hvandam at bnl.gov > Brookhaven National Laboratory > > > On 9/4/20, 04:59, "autodock-bounces at scripps.edu on behalf of Esposito Carmen" wrote: > > Hi! > > I am using the python script https://urldefense.proofpoint.com/v2/url?u=http-3A__prepare-5Fligand4.py&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=toBG7uPOawPYNuEr81UCajlWgtB_Qn6ymxLbJoFuTfk&s=yswljxPS786oN5qcesr7ZLVN13t7e593Dk1E50vwIDM&e= to convert mol2 files to pdbqt (I generate the mol2 files containing partial charges using antechamber of AmberTools20). > > pythonsh https://urldefense.proofpoint.com/v2/url?u=http-3A__prepare-5Fligand4.py&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=toBG7uPOawPYNuEr81UCajlWgtB_Qn6ymxLbJoFuTfk&s=yswljxPS786oN5qcesr7ZLVN13t7e593Dk1E50vwIDM&e= -l file.mol2 -C -o file.pdbqt > > However, I noticed that when doing the format conversion carbon atoms with the atom type CA (in the mol2) are transformed into calcium atoms (Ca, in the pdbqt file). > I attached here a couple of examples. > Is it possible that this is a bug? > > Thank you very much for your help! > > Best regards, > Carmen > > > > ________________________________________________ > --- ADL: AutoDock List --- https://urldefense.com/v3/__http://autodock.scripps.edu/mailing_list__;!!P4SdNyxKAPE!WFeaSGPsDp6rIP35Id41VTgGAH4PixH8zqZ3Q8gUvQHg3DFEMHBaNYTD77H6UPM$ --- > ________________________________________________ > --- ADL: AutoDock List --- https://urldefense.com/v3/__http://autodock.scripps.edu/mailing_list__;!!P4SdNyxKAPE!WFeaSGPsDp6rIP35Id41VTgGAH4PixH8zqZ3Q8gUvQHg3DFEMHBaNYTD77H6UPM$ --- > > > ________________________________________________ > --- ADL: AutoDock List --- https://urldefense.proofpoint.com/v2/url?u=http-3A__autodock.scripps.edu_mailing-5Flist&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=toBG7uPOawPYNuEr81UCajlWgtB_Qn6ymxLbJoFuTfk&s=8Abj2-PSBDbiuFPOWn63NeX-aCNEAtP2kiNDxGhqjkM&e= --- ________________________________________________ --- ADL: AutoDock List --- https://urldefense.com/v3/__http://autodock.scripps.edu/mailing_list__;!!P4SdNyxKAPE!WEn3f8DCbnLnbWtO2vxZMl9b16m5WCGAlsv6mmiEdISSpkSIQC8zl2IYJ-Fn6Is$ --- ________________________________________________ --- ADL: AutoDock List --- https://urldefense.com/v3/__http://autodock.scripps.edu/mailing_list__;!!P4SdNyxKAPE!TkhOlZfuqX8ODbmxzZ23CqWJHAbdj0KSQUaJWoW8lG6PNCeTljQorrWMILNh9_E$ --- ________________________________________________ --- ADL: AutoDock List --- https://urldefense.com/v3/__http://autodock.scripps.edu/mailing_list__;!!P4SdNyxKAPE!TkhOlZfuqX8ODbmxzZ23CqWJHAbdj0KSQUaJWoW8lG6PNCeTljQorrWMILNh9_E$ --- From carmen.esposito at phys.chem.ethz.ch Wed Sep 9 10:30:37 2020 From: carmen.esposito at phys.chem.ethz.ch (Esposito Carmen) Date: Wed, 9 Sep 2020 17:30:37 +0000 Subject: ADL: prepare_ligand4.py converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion In-Reply-To: <5433B249-55D4-41A6-94DA-C25CE864C55E@bnl.gov> References: <5433B249-55D4-41A6-94DA-C25CE864C55E@bnl.gov> Message-ID: Hi Huub, I actually first wrote to the amber email list and they suggested me to write to the autodock list. Alternatively, one can solve the problem at the PDB preparation step. Before I was using obabel to convert my initial sdf file (with correct protomer and tautomer) to a pdb. It was at this step that atoms were "wrongly" named, i.e. a carbon atom could happen to be named "CA". Now, I decided to use this python/rdkit function (sdf_file is assumed to contain only one molecule): from rdkit import Chem from rdkit.Chem import AllChem import subprocess sdf_file = "molecule.sdf" def sdf2pdb(sdf_file): sdf = Chem.SDMolSupplier(sdf_file)[0] mol = Chem.AddHs(sdf) AllChem.EmbedMolecule(mol) AllChem.MMFFOptimizeMolecule(mol) mol.SetProp("_Name", "LIG") elem_count = {} mi = Chem.AtomPDBResidueInfo() mi.SetResidueName('LIG') mi.SetResidueNumber(1) mi.SetIsHeteroAtom(True) mi.SetOccupancy(0.0) mi.SetTempFactor(0.0) for a in mol.GetAtoms(): n = elem_count.get(a.GetAtomicNum(), 0) n += 1 elem_count[a.GetAtomicNum()] = n n = min(n, 99) atom_name = '{0:>2s}{1:<2d}'.format(a.GetSymbol(), n) mi.SetName(atom_name) a.SetMonomerInfo(mi) Chem.rdmolfiles.MolToPDBFile(mol, '{}.pdb'.format(os.path.splitext(sdf_file)[0]), flavor=2) args_subproc = "sed -i '/CONECT/d' {}.pdb".format(os.path.splitext(sdf_file)[0]) subprocess.call(args_subproc, shell=True) Once I have the "correct" pdb, I use antechamber to generate the mol2 with AM1-BCC partial charges: antechamber -i molecule.pdb -fi pdb -o molecule.mol2 -fo mol2 -c bcc -s 2 -nc CHARGE -pf y And finally I use prepare_ligand4.py to generate the pdbqt file for autodock: pythonsh prepare_ligand4.py -l molecule.mol2 -C -o molecule.pdbqt Best wishes, Carmen ________________________________ From: autodock-bounces at scripps.edu on behalf of Van Dam, Hubertus Sent: Wednesday, September 9, 2020 7:01:45 PM To: autodock at scripps.edu Subject: Re: ADL: prepare_ligand4.py converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion Hi Carmen, I think the underlying problem is likely to be that Amber uses a MOL2 dialect. It would seem that Amber uses the atom type "ca" to select a particular set of force field parameters for Carbon atoms that are not covered by any of the other MOL2 atom types. There is enough information in the atom names and the atom types to resolve this as long as the atom names correspond to the PDB atom names. As long as that is the case it is possible to write a Tripos MOL2 to Amber MOL2 converter and vice versa without losing information so that you could actually convert either MOL2 file back to PDB. The question is where such a tool should live. I guess the best place for it to go would be the Amber Tools. However, I don't know if they accept contributed utilities, I will ask. Best wishes, Huub ----------------------------------------------------------------------------------------------------- Hubertus van Dam, 631-344-6020, hvandam at bnl.gov Brookhaven National Laboratory ?On 9/9/20, 07:01, "autodock-bounces at scripps.edu on behalf of Esposito Carmen" wrote: Hi Mihaly, Hi Huub, I agree with the comment of Huub. In addition, I want to use the mol2 file because it has the charges generated using antechamber and I want to use these charges for the docking. Anyway... I found that atoms named "CA" are defined as calcium atoms in the AutoDockTools parameter files AD4.1_bound.dat and AD4_parameters.dat. atom_par Ca 1.98 0.550 2.7700 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding Calcium atom_par CA 1.98 0.550 2.7700 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding Calcium However, I did not find yet how to solve this issue such that the prepare_ligand4.py script relies on the atom types, e.g. c3, and not on the atom names to identify elements. The easiest solution is to rename the the "CA" carbon atoms as, e.g., "C99", in the mol2 file before running the prepare_ligand4.py script ( I assume that small molecules usually have less than 100 carbon atoms; hence the "C99" atom name is unique). sed -i 's/ CA / C99/g' file.mol2 Best wishes, Carmen ________________________________ From: autodock-bounces at scripps.edu on behalf of Van Dam, Hubertus Sent: Sunday, September 6, 2020 2:11:16 AM To: autodock at scripps.edu Subject: Re: ADL: prepare_ligand4.py converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion Hi Mihaly, I am sorry but I don't think your statement is entirely correct. In PDB files how atom names are to be interpreted depends on the position in the line (see: https://urldefense.com/v3/__https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html*ATOM__;Iw!!P4SdNyxKAPE!TkhOlZfuqX8ODbmxzZ23CqWJHAbdj0KSQUaJWoW8lG6PNCeTljQorrWMGeNuImc$ ) as well as the atom name. I.e. "CA" in columns 13 and 14 is Calcium, "CA" in columns 14 and 15 is an alpha-Carbon. The other issue is that the files discussed here are MOL2 files. How the atom names in MOL2 files are to be interpreted does not have to be the same as that in PDB files. In fact a "calcium" atom with the atom type "sp3-hybridized Carbon" does not make any sense. The document that describes the MOL2 format (see: https://urldefense.com/v3/__http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf__;!!P4SdNyxKAPE!TkhOlZfuqX8ODbmxzZ23CqWJHAbdj0KSQUaJWoW8lG6PNCeTljQorrWMceE5X2I$ page 12) actually gives an alpha-Carbon as an example, suggesting that the MOL2 format allows using the PDB atom names but that the atom type has to resolve ambiguous atom names (i.e. atom_name=CA and atom_type=ca is Calcium, whereas atom_name=CA and atom_type=c.3 is an alpha-Carbon). Admittedly the MOL2 document is not very explicit about how atom names are to be interpreted, which might be a major source of confusion. Best wishes, Huub ----------------------------------------------------------------------------------------------------- Hubertus van Dam, 631-344-6020, hvandam at bnl.gov Brookhaven National Laboratory On 9/5/20, 08:23, "autodock-bounces at scripps.edu on behalf of Mezei, Mihaly" wrote: Hello, the key to the puzzle is the PDB atom name convention that the first two characters of the name is the chemical symbol. Thus, making CA into calcium is not a bug. However, not all programs recognize this - hence the confusion. Mihaly Mezei Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai Voice: (212) 659-5475. Fax: (212) 849-2456 WWW (MSSM home): https://urldefense.com/v3/__http://icahn.mssm.edu/profiles/mihaly-mezei__;!!P4SdNyxKAPE!WEn3f8DCbnLnbWtO2vxZMl9b16m5WCGAlsv6mmiEdISSpkSIQC8zl2IYFX9HOO8$ WWW (Lab home - software, publications): https://urldefense.com/v3/__http://inka.mssm.edu/*mezei__;fg!!P4SdNyxKAPE!WEn3f8DCbnLnbWtO2vxZMl9b16m5WCGAlsv6mmiEdISSpkSIQC8zl2IYqc7b-EU$ > On Sep 4, 2020, at 11:34 AM, Van Dam, Hubertus wrote: > > USE CAUTION: External Message. > > Hi Carmen, > > Sorry, I was looking at atoms 2, 3, and 4 in 3R1_pH74_netcharge.mol2. They are listed as: > > 2 C1 2.1330 -2.3280 0.5080 ca 1 UNK 0.502600 > 3 C2 1.3340 -1.2480 0.8230 ca 1 UNK -0.458600 > 4 C3 1.9460 -0.0180 0.9010 ca 1 UNK 0.698200 > > So the atom ids are fine (column 2) but the atom types are wrong (column 6). But you are right atom 9 as you stated: > > 9 CA 5.9540 0.3730 -0.1620 c3 1 UNK 0.174500 > > has the correct atom type but is erroneously converted into a Calcium atom. The observations of the both of us agree that the > > https://urldefense.proofpoint.com/v2/url?u=http-3A__prepare-5Fligand4.py&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=toBG7uPOawPYNuEr81UCajlWgtB_Qn6ymxLbJoFuTfk&s=yswljxPS786oN5qcesr7ZLVN13t7e593Dk1E50vwIDM&e= > > script determines the atom type from the atom id and incorrectly ignores the atom type. > > Fixing this problem by going by the atom type will break what the code does for atoms 2-4. However, in your examples it should be sufficient if the script checked the atom type when the atom id is ambiguous. Typical atom ids causing trouble are: > > CA > CD > CE > CF (? I seem to remember this one but don't have an example for it right now) > HO (occurs in Amber or Charmm , means Hydrogen attached to Oxygen, not Holmium) > > I think these are the most common troublemakers. > > Best wishes, > > Huub > > ----------------------------------------------------------------------------------------------------- > Hubertus van Dam, 631-344-6020, hvandam at bnl.gov > Brookhaven National Laboratory > > > On 9/4/20, 10:38, "autodock-bounces at scripps.edu on behalf of Esposito Carmen" wrote: > > Hi, > > > Thank you for your reply. > > In the mol2, the atom named CA has the correct type c3 (and also the 3D structure is correct). > > > 9 CA 5.9540 0.3730 -0.1620 c3 1 UNK 0.174500 > > > The problem occurs only when I do the format conversion. In the pdbqt: > > > ATOM 18 CA UNK d 1 5.954 0.373 -0.162 0.00 0.00 0.174 Ca > > > ...All other carbon atoms named C1, C2, C3... are correctly recognised. > > So far, I corrected this error manually by modifying the line above, i.e. adjust the spacing between 18 and CA and replace "Ca" with "Ca". > > > ATOM 18 CA UNK d 1 5.954 0.373 -0.162 0.00 0.00 0.174 C > > > Anyway, I generated the mol2 file using the antechamber program from AmberTools20. After docking, I need to run MD simulations and this is why I parametrise the molecules in the first step. In this way, I can also use the same partial charges for docking. > > > Best wishes, > > Carmen > > ________________________________ > From: autodock-bounces at scripps.edu on behalf of Van Dam, Hubertus > Sent: Friday, September 4, 2020 3:38:01 PM > To: autodock at scripps.edu > Subject: Re: ADL: https://urldefense.proofpoint.com/v2/url?u=http-3A__prepare-5Fligand4.py&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=toBG7uPOawPYNuEr81UCajlWgtB_Qn6ymxLbJoFuTfk&s=yswljxPS786oN5qcesr7ZLVN13t7e593Dk1E50vwIDM&e= converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion > > Hi Carmen, > > Where did you get the mol2 files from? In MOL2 files (see: https://urldefense.com/v3/__http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf__;!!P4SdNyxKAPE!WFeaSGPsDp6rIP35Id41VTgGAH4PixH8zqZ3Q8gUvQHg3DFEMHBaNYTDBApG5Es$ ) the atom types are supposed to be SYBYL atom types. I guess the alpha-carbons should be sp3 carbons (in most cases?) which would be indicated with C.3 (see: https://urldefense.com/v3/__http://tccc.iesl.forth.gr/education/local/quantum/molecular_modeling/guide_documents/SYBYL_data_document.html__;!!P4SdNyxKAPE!WFeaSGPsDp6rIP35Id41VTgGAH4PixH8zqZ3Q8gUvQHg3DFEMHBaNYTDODoQzyQ$ ). The atom type ca is actually Calcium. So I think the script is converting the MOL2 files correctly as far as I can see, it is just that the MOL2 files don't specify the structure as it should. > > Best wishes, > > Huub > > ----------------------------------------------------------------------------------------------------- > Hubertus van Dam, 631-344-6020, hvandam at bnl.gov > Brookhaven National Laboratory > > > On 9/4/20, 04:59, "autodock-bounces at scripps.edu on behalf of Esposito Carmen" wrote: > > Hi! > > I am using the python script https://urldefense.proofpoint.com/v2/url?u=http-3A__prepare-5Fligand4.py&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=toBG7uPOawPYNuEr81UCajlWgtB_Qn6ymxLbJoFuTfk&s=yswljxPS786oN5qcesr7ZLVN13t7e593Dk1E50vwIDM&e= to convert mol2 files to pdbqt (I generate the mol2 files containing partial charges using antechamber of AmberTools20). > > pythonsh https://urldefense.proofpoint.com/v2/url?u=http-3A__prepare-5Fligand4.py&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=toBG7uPOawPYNuEr81UCajlWgtB_Qn6ymxLbJoFuTfk&s=yswljxPS786oN5qcesr7ZLVN13t7e593Dk1E50vwIDM&e= -l file.mol2 -C -o file.pdbqt > > However, I noticed that when doing the format conversion carbon atoms with the atom type CA (in the mol2) are transformed into calcium atoms (Ca, in the pdbqt file). > I attached here a couple of examples. > Is it possible that this is a bug? > > Thank you very much for your help! > > Best regards, > Carmen > > > > ________________________________________________ > --- ADL: AutoDock List --- https://urldefense.com/v3/__http://autodock.scripps.edu/mailing_list__;!!P4SdNyxKAPE!WFeaSGPsDp6rIP35Id41VTgGAH4PixH8zqZ3Q8gUvQHg3DFEMHBaNYTD77H6UPM$ --- > ________________________________________________ > --- ADL: AutoDock List --- https://urldefense.com/v3/__http://autodock.scripps.edu/mailing_list__;!!P4SdNyxKAPE!WFeaSGPsDp6rIP35Id41VTgGAH4PixH8zqZ3Q8gUvQHg3DFEMHBaNYTD77H6UPM$ --- > > > ________________________________________________ > --- ADL: AutoDock List --- https://urldefense.proofpoint.com/v2/url?u=http-3A__autodock.scripps.edu_mailing-5Flist&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=_pOLssyMlKixy9t2NfGIeaFX83dKDBvdACoDPwc9A9s&m=toBG7uPOawPYNuEr81UCajlWgtB_Qn6ymxLbJoFuTfk&s=8Abj2-PSBDbiuFPOWn63NeX-aCNEAtP2kiNDxGhqjkM&e= --- ________________________________________________ --- ADL: AutoDock List --- https://urldefense.com/v3/__http://autodock.scripps.edu/mailing_list__;!!P4SdNyxKAPE!WEn3f8DCbnLnbWtO2vxZMl9b16m5WCGAlsv6mmiEdISSpkSIQC8zl2IYJ-Fn6Is$ --- ________________________________________________ --- ADL: AutoDock List --- https://urldefense.com/v3/__http://autodock.scripps.edu/mailing_list__;!!P4SdNyxKAPE!TkhOlZfuqX8ODbmxzZ23CqWJHAbdj0KSQUaJWoW8lG6PNCeTljQorrWMILNh9_E$ --- ________________________________________________ --- ADL: AutoDock List --- https://urldefense.com/v3/__http://autodock.scripps.edu/mailing_list__;!!P4SdNyxKAPE!TkhOlZfuqX8ODbmxzZ23CqWJHAbdj0KSQUaJWoW8lG6PNCeTljQorrWMILNh9_E$ --- ________________________________________________ --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list --- From diogo.stmart at gmail.com Wed Sep 9 23:34:42 2020 From: diogo.stmart at gmail.com (Diogo Martins) Date: Wed, 9 Sep 2020 23:34:42 -0700 Subject: ADL: Help In-Reply-To: <689384481.786122.1555488008048@mail.yahoo.com> References: <689384481.786122.1555488008048.ref@mail.yahoo.com> <689384481.786122.1555488008048@mail.yahoo.com> Message-ID: Hi Shabnam, The help pages cover the topics of your questions, I recommend going through them: http://autodock.scripps.edu/faqs-help Best regards, On Wed, 9 Sep 2020 at 20:45, sarah sarahii wrote: > Dear Researchers > Hello, > > I have a question about the interpretation of AutoDock(4) docking results. > I got the docking results with high RMSD. However, I even performed another > docking with the ligand, which was existed in the basic file of the protein > (mofegiline with one subunite of 2vz2), but I again found a high RMSD. I > want to ask you please help me about the questions: > > 1. How should I define the "reference structure" to obtain the result with > low RMSD. > > 2. Is it necessary to have low RMSD in result of docking or not? > > 3. Please mention the steps in details to define the "reference structure" > in the related file (or files) to reach the perfect and correct results of > docking (with Autodock 4) in accompany with low RMSD. > > I thank you > Sincerely Yours, > Shabnam > > > ________________________________________________ > --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list --- > > From hvandam at bnl.gov Thu Sep 10 12:15:01 2020 From: hvandam at bnl.gov (Van Dam, Hubertus) Date: Thu, 10 Sep 2020 19:15:01 +0000 Subject: ADL: Problem about autodock Message-ID: Hi Apisara, When you run autogrid4.exe -p file.gpf -l file.glg do you get any error messages? I don't use Autodock on Windows machines, so I am not entirely sure how that works, but on Windows machines the native way to provide command line options would be autogrid4.exe /p file.gpf /l file.glg although it seems that the hyphen notation also works in some cases (maybe it depends on the code and I don't know if autogrid builds differently for Windows). Either way, any error messages produced would be very helpful. If the autogrid produced any "file.glg" log file then this would contain the error messages. If for some reason that autogrid program cannot run at all, I would expect to see something in your terminal window that provides some clues as to why the program won't run. Best wishes, Huub ----------------------------------------------------------------------------------------------------- Hubertus van Dam, 631-344-6020, hvandam at bnl.gov Brookhaven National Laboratory ?On 9/9/20, 23:48, "autodock-bounces at scripps.edu on behalf of ?????????? ???????" wrote: ---------- Forwarded message --------- ???: ?????????? ??????? Date: ?. 20 ??.?. 2020 ???? 20:11 Subject: Problem about autodock To: Dear sir My name is Apisara Baicharoen. I am a student. I have problem with autodock for docking. First, my molecule is deformed. This molecule is trimethoprim. That is shown below. Last, I followed https://urldefense.com/v3/__http://www.youtube.com/watch?v=kEEOLK_N0s__;!!P4SdNyxKAPE!T6xGt3rwEdVjqVM5UQyuGryFPts0VL7mBbbmRb6xcPEClzcDg6eLF1eMEUA3-u4$ for docking . However, i could not save file.glg and file.dlg in order to continue next step for docking. In addition, I tried to use command in pc with code autogrid4.exe -p file.gpf -l file.glg but it is not successful. Please help me. This is my project for master degree. Your sincerely Sent from my iPhone From hvandam at bnl.gov Thu Sep 10 12:21:20 2020 From: hvandam at bnl.gov (Van Dam, Hubertus) Date: Thu, 10 Sep 2020 19:21:20 +0000 Subject: ADL: Unable to create .glg file Message-ID: <3935F9C0-79EB-460E-96BB-40BC5FDDEE32@bnl.gov> Hi Vineeta, I am sorry but your screenshot is not being forwarded. Best wishes, Huub ----------------------------------------------------------------------------------------------------- Hubertus van Dam, 631-344-6020, hvandam at bnl.gov Brookhaven National Laboratory ?On 9/9/20, 23:48, "autodock-bounces at scripps.edu on behalf of vineeta gupta" wrote: Hello everyone, I'm Vineeta Gupta from Lucknow, India. I want to share an issue occurring while using cygwin commands to run autodock. I'm using laptop of 64 bit home basic, windows 8. I have downloaded required softwares and files from the official website of Scripps research institute and properly installed, but not able to create .glg file. I'm sending herewith screenshot of cygwin command line window. Kindly give your expert opinion. Thanx. From ricksher at gmail.com Thu Sep 10 13:48:26 2020 From: ricksher at gmail.com (Rick Sheridan) Date: Thu, 10 Sep 2020 23:48:26 +0300 Subject: ADL: =?utf-8?q?Where_to_find_a_protein_when_it=E2=80=99s_not_in_t?= =?utf-8?q?he_PDB=3F?= Message-ID: Hi folks - does anyone know where can be found a pdb for OATPA12 (associated gene SLCO1A2)? The PDB doesn?t have it: http://www.rcsb.org/pdb/protein/P46721?chromosome=chr12&range=21428294&v=hg37 Best, Rick -- -- ******************************************************************** Rick Sheridan EMSKE Phytochem Head of R&D Whatsapp: +1-551-285-8136 www.linkedin.com/in/ricksheridan Skype:ricksher16 ******************************************************************** From bushraistaj at gmail.com Thu Sep 10 13:52:30 2020 From: bushraistaj at gmail.com (bushra TAJ) Date: Thu, 10 Sep 2020 23:52:30 +0300 Subject: ADL: =?utf-8?q?Where_to_find_a_protein_when_it=E2=80=99s_not_in_t?= =?utf-8?q?he_PDB=3F?= In-Reply-To: References: Message-ID: Hello dear In that case you will take its primary sequence and blast to find the closest possible match in case that closest match is in the PDB repository you can proceed to homology modeling than you are all good to go Best of luck On Thu, Sep 10, 2020 at 11:50 PM Rick Sheridan wrote: > Hi folks - does anyone know where can be found a pdb for OATPA12 > (associated gene SLCO1A2)? > > The PDB doesn?t have it: > > > http://www.rcsb.org/pdb/protein/P46721?chromosome=chr12&range=21428294&v=hg37 > > Best, > Rick > -- > -- > ******************************************************************** > Rick Sheridan > EMSKE Phytochem > Head of R&D > Whatsapp: +1-551-285-8136 > www.linkedin.com/in/ricksheridan > > Skype:ricksher16 > ******************************************************************** > ________________________________________________ > --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list --- From edmundmarinelli at gmail.com Thu Sep 10 19:58:09 2020 From: edmundmarinelli at gmail.com (Edmund Marinelli) Date: Thu, 10 Sep 2020 19:58:09 -0700 Subject: ADL: Attempting to create flexible portion of receptor for Autodock 4.2 and Autodock Vina Message-ID: I'm using Autodock Tools 1.57. I prepared the receptor as appropriate and was able to write the PDBQT file using the File ....Save.....Write PDBQT. It seemed to work fine , giving the message that the Autodock atom types were added. Then I wanted to create the flexible pdbqt file. Note that you have to create the flexible pdbqt file before the rigid. If you try to create the rigid pdbqt file first the program returns the message that the flexible pdbqt files must be prepared first. OK: After writing the pbdqt for the receptor I did the following: Flexible residues --> Input --> Choose macromolecule. I chose the macromolecule. Then in the dashboard I selected one residue as a test. In the viewing pane the residue was highlighted. With the residue highlighted I did the following: Flexible Resides --> Choose torsions in currently selected residues. The program immediately closed with no error message given. I don't know if my procedure is incorrect. Has anyone else tried flexible docking using Autodock Tools version 1.57? Is there another way to do this ? I would like to perform docking with flexible sidechains in the pocket residues of the receptor. Has anyone been able to do this in Autodock 4.2 or in Autodock 4, or with Autodock Vina or with an earlier version of Autodock tools? Is there any worked example or tutorial out there? Any help would be appreciated. If the syntax of a sample flexible.pdbqt file exists perhaps I would be able to use it to construct my own file , hence avoiding the problems of generating it from within Autodock tools , as there seems to be a problem. Ed From timolivermaier at gmail.com Thu Sep 10 21:13:34 2020 From: timolivermaier at gmail.com (Tim M.) Date: Fri, 11 Sep 2020 06:13:34 +0200 Subject: ADL: Attempting to create flexible portion of receptor for Autodock 4.2 and Autodock Vina In-Reply-To: References: Message-ID: Hello Edmund, I encountered the same error using current AutoDock Tools version with Windows10. I reasoned that it might be an 32bit/64bit issue. It worked with ubuntu for me. So if thats an option you can try using the Linux version. Best Regards Tim Edmund Marinelli schrieb am Fr., 11. Sept. 2020, 05:00: > I'm using Autodock Tools 1.57. I prepared the receptor as appropriate and > was able to write the PDBQT file using the File ....Save.....Write PDBQT. > It seemed to work fine , giving the message that the Autodock atom types > were added. Then I wanted to create the flexible pdbqt file. Note that > you have to create the flexible pdbqt file before the rigid. If you try to > create the rigid pdbqt file first the program returns the message that the > flexible pdbqt files must be prepared first. > > OK: After writing the pbdqt for the receptor I did the following: Flexible > residues --> Input --> Choose macromolecule. I chose the macromolecule. > Then in the dashboard I selected one residue as a test. In the viewing > pane the residue was highlighted. With the residue highlighted I did the > following: Flexible Resides --> Choose torsions in currently selected > residues. The program immediately closed with no error message given. I > don't know if my procedure is incorrect. Has anyone else tried flexible > docking using Autodock Tools version 1.57? > > Is there another way to do this ? I would like to perform docking with > flexible sidechains in the pocket residues of the receptor. Has anyone > been able to do this in Autodock 4.2 or in Autodock 4, or with Autodock > Vina or with an earlier version of Autodock tools? > > Is there any worked example or tutorial out there? Any help would be > appreciated. > > If the syntax of a sample flexible.pdbqt file exists perhaps I would be > able to use it to construct my own file , hence avoiding the problems of > generating it from within Autodock tools , as there seems to be a > problem. > > Ed > ________________________________________________ > --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list --- > > From ricksher at gmail.com Fri Sep 11 04:51:07 2020 From: ricksher at gmail.com (Rick Sheridan) Date: Fri, 11 Sep 2020 14:51:07 +0300 Subject: ADL: =?utf-8?q?Where_to_find_a_protein_when_it=E2=80=99s_not_in_t?= =?utf-8?q?he_PDB=3F?= In-Reply-To: References: Message-ID: Thanks - (and typo correction-> OATP1A2 ) On Thu, 10 Sep 2020 at 11:53 PM, bushra TAJ wrote: > Hello dear > In that case you will take its primary sequence and blast to find the > closest possible match > in case that closest match is in the PDB repository you can proceed to > homology modeling > than you are all good to go > Best of luck > > On Thu, Sep 10, 2020 at 11:50 PM Rick Sheridan wrote: > > > Hi folks - does anyone know where can be found a pdb for OATPA12 > > (associated gene SLCO1A2)? > > > > The PDB doesn?t have it: > > > > > > > http://www.rcsb.org/pdb/protein/P46721?chromosome=chr12&range=21428294&v=hg37 > > > > Best, > > Rick > > -- > > -- > > ******************************************************************** > > Rick Sheridan > > EMSKE Phytochem > > Head of R&D > > Whatsapp: +1-551-285-8136 > > www.linkedin.com/in/ricksheridan > > > > Skype:ricksher16 > > ******************************************************************** > > ________________________________________________ > > --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list --- > ________________________________________________ > --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list --- -- -- ******************************************************************** Rick Sheridan EMSKE Phytochem Head of R&D Whatsapp: +1-551-285-8136 www.linkedin.com/in/ricksheridan Skype:ricksher16 ******************************************************************** From ramramic at gmail.com Fri Sep 11 05:05:36 2020 From: ramramic at gmail.com (Ishwar Chandra) Date: Fri, 11 Sep 2020 17:35:36 +0530 Subject: ADL: =?utf-8?q?Where_to_find_a_protein_when_it=E2=80=99s_not_in_t?= =?utf-8?q?he_PDB=3F?= In-Reply-To: References: Message-ID: Hi, Put your sequence in Swiss model (https://swissmodel.expasy.org/) and you will get protein structure. best regards ishwar On Fri, Sep 11, 2020 at 5:22 PM Rick Sheridan wrote: > Thanks - (and typo correction-> OATP1A2 ) > > On Thu, 10 Sep 2020 at 11:53 PM, bushra TAJ wrote: > > > Hello dear > > In that case you will take its primary sequence and blast to find the > > closest possible match > > in case that closest match is in the PDB repository you can proceed to > > homology modeling > > than you are all good to go > > Best of luck > > > > On Thu, Sep 10, 2020 at 11:50 PM Rick Sheridan > wrote: > > > > > Hi folks - does anyone know where can be found a pdb for OATPA12 > > > (associated gene SLCO1A2)? > > > > > > The PDB doesn?t have it: > > > > > > > > > > > > http://www.rcsb.org/pdb/protein/P46721?chromosome=chr12&range=21428294&v=hg37 > > > > > > Best, > > > Rick > > > -- > > > -- > > > ******************************************************************** > > > Rick Sheridan > > > EMSKE Phytochem > > > Head of R&D > > > Whatsapp: +1-551-285-8136 > > > www.linkedin.com/in/ricksheridan > > > > > > Skype:ricksher16 > > > ******************************************************************** > > > ________________________________________________ > > > --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list > --- > > ________________________________________________ > > --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list --- > > -- > -- > ******************************************************************** > Rick Sheridan > EMSKE Phytochem > Head of R&D > Whatsapp: +1-551-285-8136 > www.linkedin.com/in/ricksheridan > > Skype:ricksher16 > ******************************************************************** > ________________________________________________ > --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list --- From DouglasR.Houston at ed.ac.uk Fri Sep 11 05:07:33 2020 From: DouglasR.Houston at ed.ac.uk (HOUSTON Douglas) Date: Fri, 11 Sep 2020 12:07:33 +0000 Subject: ADL: =?windows-1252?q?Where_to_find_a_protein_when_it=92s_not_in_?= =?windows-1252?q?the_PDB=3F?= In-Reply-To: References: , Message-ID: In fact, you can BLAST search the PDB directly: https://www.rcsb.org/search/advanced ________________________________ From: autodock-bounces at scripps.edu on behalf of Rick Sheridan Sent: 11 September 2020 12:51 To: autodock at scripps.edu Subject: Re: ADL: Where to find a protein when it?s not in the PDB? Thanks - (and typo correction-> OATP1A2 ) On Thu, 10 Sep 2020 at 11:53 PM, bushra TAJ wrote: > Hello dear > In that case you will take its primary sequence and blast to find the > closest possible match > in case that closest match is in the PDB repository you can proceed to > homology modeling > than you are all good to go > Best of luck > > On Thu, Sep 10, 2020 at 11:50 PM Rick Sheridan wrote: > > > Hi folks - does anyone know where can be found a pdb for OATPA12 > > (associated gene SLCO1A2)? > > > > The PDB doesn?t have it: > > > > > > > http://www.rcsb.org/pdb/protein/P46721?chromosome=chr12&range=21428294&v=hg37 > > > > Best, > > Rick > > -- > > -- > > ******************************************************************** > > Rick Sheridan > > EMSKE Phytochem > > Head of R&D > > Whatsapp: +1-551-285-8136 > > www.linkedin.com/in/ricksheridan > > > > Skype:ricksher16 > > ******************************************************************** > > ________________________________________________ > > --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list --- > ________________________________________________ > --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list --- -- -- ******************************************************************** Rick Sheridan EMSKE Phytochem Head of R&D Whatsapp: +1-551-285-8136 www.linkedin.com/in/ricksheridan Skype:ricksher16 ******************************************************************** ________________________________________________ --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list --- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From sanner at scripps.edu Fri Sep 11 08:30:57 2020 From: sanner at scripps.edu (Michel Sanner) Date: Fri, 11 Sep 2020 15:30:57 +0000 Subject: ADL: Attempting to create flexible portion of receptor for Autodock 4.2 and Autodock Vina Message-ID: <16264507-B1A4-4D05-A7ED-4A50BC3EFB61@scripps.edu> Hi Ed You can you AutoGridFR (AGFR) to prepare your receptor (with flexible side chains) and generate the AutoDock affinity maps. AGFR will generate a .trg file which you can use directly for docking with AutoDockFR (ADFR) or you can unzip to extract the actual affinity maps that you can use with AutoDock4. You can download the ADFRsuite at https://ccsb.scripps.edu/adfr/downloads/ (contains both AGFR and ADFR among other tools) There is a tutorial for preparing maps for a receptor with flexible side chains at https://ccsb.scripps.edu/adfr/documentation/ I hope this helps -Michel From: on behalf of Edmund Marinelli Reply-To: "autodock at scripps.edu" Date: Thursday, September 10, 2020 at 7:59 PM To: "autodock at scripps.edu" Subject: ADL: Attempting to create flexible portion of receptor for Autodock 4.2 and Autodock Vina I'm using Autodock Tools 1.57. I prepared the receptor as appropriate and was able to write the PDBQT file using the File ....Save.....Write PDBQT. It seemed to work fine , giving the message that the Autodock atom types were added. Then I wanted to create the flexible pdbqt file. Note that you have to create the flexible pdbqt file before the rigid. If you try to create the rigid pdbqt file first the program returns the message that the flexible pdbqt files must be prepared first. OK: After writing the pbdqt for the receptor I did the following: Flexible residues --> Input --> Choose macromolecule. I chose the macromolecule. Then in the dashboard I selected one residue as a test. In the viewing pane the residue was highlighted. With the residue highlighted I did the following: Flexible Resides --> Choose torsions in currently selected residues. The program immediately closed with no error message given. I don't know if my procedure is incorrect. Has anyone else tried flexible docking using Autodock Tools version 1.57? Is there another way to do this ? I would like to perform docking with flexible sidechains in the pocket residues of the receptor. Has anyone been able to do this in Autodock 4.2 or in Autodock 4, or with Autodock Vina or with an earlier version of Autodock tools? Is there any worked example or tutorial out there? Any help would be appreciated. If the syntax of a sample flexible.pdbqt file exists perhaps I would be able to use it to construct my own file , hence avoiding the problems of generating it from within Autodock tools , as there seems to be a problem. Ed ________________________________________________ --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list --- From ricksher at gmail.com Fri Sep 11 11:14:36 2020 From: ricksher at gmail.com (Rick Sheridan) Date: Fri, 11 Sep 2020 21:14:36 +0300 Subject: ADL: =?utf-8?q?Where_to_find_a_protein_when_it=E2=80=99s_not_in_t?= =?utf-8?q?he_PDB=3F?= In-Reply-To: References: Message-ID: Ah understood, many thanks all! =) On Fri, 11 Sep 2020 at 3:52 PM, HOUSTON Douglas wrote: > In fact, you can BLAST search the PDB directly: > > https://www.rcsb.org/search/advanced > > > ________________________________ > From: autodock-bounces at scripps.edu on > behalf of Rick Sheridan > Sent: 11 September 2020 12:51 > To: autodock at scripps.edu > Subject: Re: ADL: Where to find a protein when it?s not in the PDB? > > Thanks - (and typo correction-> OATP1A2 ) > > On Thu, 10 Sep 2020 at 11:53 PM, bushra TAJ wrote: > > > Hello dear > > In that case you will take its primary sequence and blast to find the > > closest possible match > > in case that closest match is in the PDB repository you can proceed to > > homology modeling > > than you are all good to go > > Best of luck > > > > On Thu, Sep 10, 2020 at 11:50 PM Rick Sheridan > wrote: > > > > > Hi folks - does anyone know where can be found a pdb for OATPA12 > > > (associated gene SLCO1A2)? > > > > > > The PDB doesn?t have it: > > > > > > > > > > > > http://www.rcsb.org/pdb/protein/P46721?chromosome=chr12&range=21428294&v=hg37 > > > > > > Best, > > > Rick > > > -- > > > -- > > > ******************************************************************** > > > Rick Sheridan > > > EMSKE Phytochem > > > Head of R&D > > > Whatsapp: +1-551-285-8136 > > > www.linkedin.com/in/ricksheridan< > http://www.linkedin.com/in/ricksheridan> > > > > > > Skype:ricksher16 > > > ******************************************************************** > > > ________________________________________________ > > > --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list > --- > > ________________________________________________ > > --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list --- > > -- > -- > ******************************************************************** > Rick Sheridan > EMSKE Phytochem > Head of R&D > Whatsapp: +1-551-285-8136 > www.linkedin.com/in/ricksheridan > > Skype:ricksher16 > ******************************************************************** > ________________________________________________ > --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list --- > The University of Edinburgh is a charitable body, registered in Scotland, > with registration number SC005336. > ________________________________________________ > --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list --- > > -- -- ******************************************************************** Rick Sheridan EMSKE Phytochem Head of R&D Whatsapp: +1-551-285-8136 www.linkedin.com/in/ricksheridan Skype:ricksher16 ******************************************************************** From edmundmarinelli at gmail.com Sat Sep 12 14:38:25 2020 From: edmundmarinelli at gmail.com (Edmund R Marinelli) Date: Sat, 12 Sep 2020 14:38:25 -0700 (MST) Subject: ADL: Attempting to create flexible portion of receptor for Autodock 4.2 and Autodock Vina In-Reply-To: References: Message-ID: <1599946705442-0.post@n2.nabble.com> Hi Tim: Seems to work with ADT v 1.56. Hopefully it can be fixed in 1.57? -- Sent from: http://autodock.1369657.n2.nabble.com/ From edmundmarinelli at gmail.com Sat Sep 12 18:20:36 2020 From: edmundmarinelli at gmail.com (Edmund R Marinelli) Date: Sat, 12 Sep 2020 18:20:36 -0700 (MST) Subject: ADL: Receptor file in 2016 Nature Protocols Paper Message-ID: <1599960036333-0.post@n2.nabble.com> The paper Computational protein-ligand docking and virtual drug screening with the AutoDock suite , Nat Protoc. 2016 May ; 11(5): 905?919. doi:10.1038/nprot.2016.051 is a very nice paper. In the supplementary material there is a receptor file 1iep_receptorH.pdb . As we have been cautioned to inspect the input files, I did so. Here are the first few lines: REMARK 4 XXXX COMPLIES WITH FORMAT V. 2.0 ATOM 3429 HB2 SER A 438 13.612 67.338 33.314 1.00 0.00 H ATOM 1 N MET A 225 19.353 41.547 -3.887 1.00 72.26 N ATOM 2 HN1 MET A 225 19.594 42.398 -3.380 1.00 0.00 H ATOM 3 HN2 MET A 225 18.908 40.869 -3.268 1.00 0.00 H Why is Atom 3429 for SER A 438 listed as the first atom? I did notice that atom 3429 entry is NOT listed elsewhere in the file, so there is no duplication. Does the order of appearance of the coordinates matter or could conceivable all coordinates be given in a random order so long as the data in each line are correct? Finally, is there a detailed explanation of all atom types and each of the fields for pdbqt files available. -- Sent from: http://autodock.1369657.n2.nabble.com/ From narendrag1995 at gmail.com Sun Sep 13 05:11:24 2020 From: narendrag1995 at gmail.com (Nari Narendra) Date: Sun, 13 Sep 2020 17:41:24 +0530 Subject: ADL: (no subject) Message-ID: Respected Sir/Madam Hello everyone, I have a question regarding charges in autodock. why we will use Kollman charges for protein and gasteger charges for ligands Thank you Regards Narendra From edmundmarinelli at gmail.com Mon Sep 14 20:21:34 2020 From: edmundmarinelli at gmail.com (Edmund R Marinelli) Date: Mon, 14 Sep 2020 20:21:34 -0700 (MST) Subject: ADL: Malwarebytes and MGLTools Uninstall.exe Message-ID: <1600140094773-0.post@n2.nabble.com> Hello: I have Malwarebytes (malware detection program). Malwarebytes flagged the Uninstall.exe files for several MGLTools versions as possibly problematic based on a Heuristic algorithm. Do you have any idea why the uninstall.exe for MGLTools different versions would be flagged as possible malware? Though its not a Scripps "product" I was surprised to see that upon going to the GalaxyDock website Malware bytes stopped access to the site indicating possible malware there. I mention this because I am wondering if perhaps modeling sites are being targeted by malware creators. Any thoughts you have would be appreciated. -- Sent from: http://autodock.1369657.n2.nabble.com/ From jmsstarlight at gmail.com Tue Sep 15 02:13:11 2020 From: jmsstarlight at gmail.com (James Starlight) Date: Tue, 15 Sep 2020 11:13:11 +0200 Subject: ADL: Virtual screening with Autodock Message-ID: Hello there I am performing virtual screening of millions of small compounds docked to several receptors. As the result of 20 repetitions normally carried out for each complex, I get either a ligand pose with the lowest energy within a small cluster (a few poses) or alternatively a "larger" cluster (containing several similar poses) possessing higher free energy. What of these two outputs could be taken into account, assuming that I am dealing with HT blind docking runs? Does the distribution of the cluster correspond implicitly to the entropy term of dG (taking into account flexibility of the ligand)?? Many thanks in advance ! Sincerely yours, prof. James St. From josh at rosabio.tech Tue Sep 15 03:51:37 2020 From: josh at rosabio.tech (josh at rosabio.tech) Date: Tue, 15 Sep 2020 11:51:37 +0100 Subject: ADL: Grid box spacing in Autodock 4 Message-ID: Hey guys, Apologies for sending this again, I asked a similar question regarding Autodock Vina last week but I cannot seem to work out how to reply on the same forum (!!), so I am just posting it here, sorry. I am wondering how the Grid box spacing influences the results of Autodock 4. I understand Vina fixes spacing at 0.375 so changing this has no influence on the result, but what about AD4? Will a grid box with a certain spacing run faster than a grid box of the same size using a larger spacing (and therefore larger number of grid points)? What is the purpose of spacing for the docking run? Any comment would be greatly appreciated. Many thanks in advance, Josh From poti.adam.levente at ttk.mta.hu Thu Sep 17 08:32:14 2020 From: poti.adam.levente at ttk.mta.hu (poti.adam.levente at ttk.mta.hu) Date: Thu, 17 Sep 2020 17:32:14 +0200 Subject: ADL: scheduler problem Message-ID: Dear all, we would like to run Raccoon2 on a Linux server, which has SGE as the grid scheduler. However, when we set up the server in the Raccoon2 GUI, the scheduler is detected to be PBS. According to the manual, SGE is also supported, is there a way to manually switch to SGE? Thank you for your help, ?d?m From edmundmarinelli at gmail.com Thu Sep 17 14:27:43 2020 From: edmundmarinelli at gmail.com (Edmund R Marinelli) Date: Thu, 17 Sep 2020 14:27:43 -0700 (MST) Subject: ADL: AutoDock 4 and halogenated compounds Message-ID: <1600378063722-0.post@n2.nabble.com> AutoDock VinaXB was developed to provide improved scoring for halogen containing compounds. Does AutoDock 4.2 also have an analogous parameter set that provides improved scoring for halogen containing compounds? -- Sent from: http://autodock.1369657.n2.nabble.com/ From diogo.stmart at gmail.com Thu Sep 17 14:45:21 2020 From: diogo.stmart at gmail.com (Diogo Martins) Date: Thu, 17 Sep 2020 14:45:21 -0700 Subject: ADL: AutoDock 4 and halogenated compounds In-Reply-To: <1600378063722-0.post@n2.nabble.com> References: <1600378063722-0.post@n2.nabble.com> Message-ID: No. In AutoDock 4.2 interactions involving halogens are described by the vdW, electrostatic and desolvation potentials. Halogens carry a single partial charge at the atomic center. On Thu, 17 Sep 2020 at 14:29, Edmund R Marinelli wrote: > AutoDock VinaXB was developed to provide improved scoring for halogen > containing compounds. Does AutoDock 4.2 also have an analogous parameter > set that provides improved scoring for halogen containing compounds? > > > > -- > Sent from: http://autodock.1369657.n2.nabble.com/ > > > ________________________________________________ > --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list --- > > From diogo.stmart at gmail.com Thu Sep 17 14:51:22 2020 From: diogo.stmart at gmail.com (Diogo Martins) Date: Thu, 17 Sep 2020 14:51:22 -0700 Subject: ADL: Grid box spacing in Autodock 4 In-Reply-To: References: Message-ID: Hi Josh, I don't think it makes a difference in terms of docking runtime. Autogrid will take longer if more grid points are required. You can find more information about the spacing here: http://autodock.scripps.edu/faqs-help/manual/autodock-3-user-s-guide/AutoDock3.0.5_UserGuide.pdf Best regards, On Tue, 15 Sep 2020 at 03:53, wrote: > > Hey guys, > > > Apologies for sending this again, I asked a similar question regarding > Autodock Vina last week but I cannot seem to work out how to reply on > the > same forum (!!), so I am just posting it here, sorry. > > > I am wondering how the Grid box spacing influences the results of > Autodock > 4. I understand Vina fixes spacing at 0.375 so changing this has no > influence on the result, but what about AD4? Will a grid box with a > certain > spacing run faster than a grid box of the same size using a larger > spacing > (and therefore larger number of grid points)? What is the purpose of > spacing > for the docking run? > > > Any comment would be greatly appreciated. > > > Many thanks in advance, > > > Josh > ________________________________________________ > --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list --- > > From edmundmarinelli at gmail.com Fri Sep 18 23:02:30 2020 From: edmundmarinelli at gmail.com (Edmund R Marinelli) Date: Fri, 18 Sep 2020 23:02:30 -0700 (MST) Subject: ADL: Active torsions vs TORSDOF number Message-ID: <1600495350321-0.post@n2.nabble.com> Hello: I created a ligand file using MGL tools v 1.56. TORSDOF was set to 7 and active torsions was 7. In MGLTools I then went back and modified the torsions by allowing rotation of amide bonds. The new pdbqt file showed 8 active torsions but the TORSDOF value at the end of the pdbqt file was still 7. Shouldn't the TORSDOF value change to 8? If the TORSDOF value is left at 7 and the number of specified active torsions in the pdbqt file is 8 will Autodock 4.2 employ the specified 8 active torsions in the docking run? -- Sent from: http://autodock.1369657.n2.nabble.com/ From diogo.stmart at gmail.com Sat Sep 19 10:34:52 2020 From: diogo.stmart at gmail.com (Diogo Martins) Date: Sat, 19 Sep 2020 10:34:52 -0700 Subject: ADL: Active torsions vs TORSDOF number In-Reply-To: <1600495350321-0.post@n2.nabble.com> References: <1600495350321-0.post@n2.nabble.com> Message-ID: Hello, The bonds that are allowed to rotate are defined by the BRANCH/ENDBRANCH keywords. The TORSDOF is used to calculate the loss of conformational entropy upon binding. Best regards On Fri, Sep 18, 2020 at 11:04 PM Edmund R Marinelli < edmundmarinelli at gmail.com> wrote: > Hello: I created a ligand file using MGL tools v 1.56. TORSDOF was set > to 7 > > and active torsions was 7. In MGLTools I then went back and modified the > > torsions by allowing rotation of amide bonds. The new pdbqt file showed 8 > > active torsions but the TORSDOF value at the end of the pdbqt file was > still > > 7. Shouldn't the TORSDOF value change to 8? If the TORSDOF value is left > > at 7 and the number of specified active torsions in the pdbqt file is 8 > will > > Autodock 4.2 employ the specified 8 active torsions in the docking run? > > > > > > > > -- > > Sent from: http://autodock.1369657.n2.nabble.com/ > > > > > > ________________________________________________ > > --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list --- > > > > From alejandergo at iata.csic.es Mon Sep 21 00:45:08 2020 From: alejandergo at iata.csic.es (ALEJANDRO HERES GOZALBES) Date: Mon, 21 Sep 2020 09:45:08 +0200 Subject: ADL: Analysing AutoDock Results, H bonds Message-ID: <20200921094508.Horde.vYdadUnIqbyQ2Y3c9n23zD-@webmail.csic.es> Greetings, I have performed a Molecular Docking test with AutoDock. I don't know how to interpret certain letters of the encoding, for example, I understand that 2q1l:D:ALA599:HN : pravastatin: : 0:O,O means that in the D chain, the ALA599 residue from the receptor is the one involved in the formation of the H bond with the 0:O,O group from pravastatin, but I do not know what "HN" means nor 0: O,O on the pravastatin side. Likewise, does the fact that the data is arranged in two columns mean that donors go to one side and acceptors to the other? If so, which side corresponds to a donor / acceptor species? Thanks in advance From horse16031603 at yahoo.co.jp Mon Sep 21 22:40:59 2020 From: horse16031603 at yahoo.co.jp (horse16031603 at yahoo.co.jp) Date: Tue, 22 Sep 2020 14:40:59 +0900 (JST) Subject: ADL: Q: Vina virtual screening with 9873 molecules downloaded from ZINC15 References: <984785871.206998.1600753259137.JavaMail.yahoo.ref@mail.yahoo.co.jp> Message-ID: <984785871.206998.1600753259137.JavaMail.yahoo@mail.yahoo.co.jp> Dearhonorable AutoDock users: ? I downloaded 9873 small moleculesfrom ZINC, and I did my AutoDock Vina with failure. The following is therelated files and troubles. ? ?????(Note1)? File?9783 ligand 3D pdbqt ?molecules downloaded from ZINC15 (it shows thefirst molecule and the last one) ? ? MODEL???????1 REMARK? Name= ZINC000000011175 REMARK? 5active torsions: REMARK?status: ('A' for Active; 'I' for Inactive) REMARK???1? A??? between atoms: C1_1? and?C2_2 REMARK???2? A??? between atoms: N4_4? and?C5_5 REMARK???3? A??? between atoms: C8_8? and?C10_10 REMARK???4? A??? between atoms: C10_10? and?O11_11 REMARK???5? A??? between atoms: C13_13? and?O15_15 REMARK???????????????????????????x?????? y??????z???? vdW? Elec??????q??? Type REMARK???????????????????????? _______ ______________ _____ _____??? ______ ____ ROOT ATOM?????1? C1? <0> A??1????? -0.018?? 1.503??0.010? 0.00? 0.00???+0.140 C ATOM?????2? C2? <0> A??1?????? 0.002? -0.004??0.002? 0.00? 0.00???-0.270 C ATOM?????3? C3? <0> A??1????? -1.153? -0.704??0.004? 0.00? 0.00???+0.370 C ATOM?????4? N4? <0> A??1????? -1.116? -2.072?-0.004? 0.00? 0.00???-0.520 N ATOM????13? C16 <0> A?? 1??????0.060? -2.726? -0.013?0.00? 0.00??? +0.710 C ATOM????14? O17 <0> A?? 1??????0.069? -3.942? -0.020?0.00? 0.00??? -0.540 OA ATOM????15? N18 <0> A?? 1??????1.226? -2.053? -0.016?0.00? 0.00??? -0.660 N ATOM????16? C19 <0> A?? 1??????1.232? -0.705? -0.013?0.00? 0.00??? +0.550 C ATOM????17? O20 <0> A?? 1??????2.287? -0.095? -0.016?0.00? 0.00??? -0.510 OA ATOM????20? H31 <0> A?? 1??????2.064? -2.540? -0.023?0.00? 0.00??? +0.430 HD ENDROOT BRANCH??4?? 5 ATOM?????5? C5? <0> A??1????? -2.369? -2.831?-0.002? 0.00? 0.00???+0.440 C ATOM?????6? O7? <0> A??1????? -3.500? -1.935?-0.062? 0.00? 0.00???-0.360 OA ATOM?????7? C8? <0> A??1????? -4.597? -2.740?-0.547? 0.00? 0.00???+0.170 C ATOM????10? C12 <0> A?? 1??? ??-3.978?-3.629? -1.647? 0.00?0.00??? +0.010 C ATOM????11? C13 <0> A?? 1?????-2.477? -3.693? -1.280?0.00? 0.00??? +0.160 C BRANCH?11? 12 ATOM????12? O15 <0> A?? 1?????-1.680? -3.138? -2.328?0.00? 0.00??? -0.550 OA ATOM????19? H30 <0> A?? 1???? ?-1.759?-3.605? -3.171? 0.00?0.00??? +0.390 HD ENDBRANCH?11? 12 BRANCH??7?? 8 ATOM?????8? C10 <0> A?? 1?????-5.693? -1.847? -1.133?0.00? 0.00??? +0.210 C BRANCH??8?? 9 ATOM?????9? O11 <0> A?? 1?????-6.280? -1.066? -0.090?0.00? 0.00??? -0.570 OA ATOM????18? H27 <0> A?? 1?????-6.985? -0.476? -0.391?0.00? 0.00??? +0.390 HD ENDBRANCH??8?? 9 ENDBRANCH??7?? 8 ENDBRANCH??4?? 5 TORSDOF 4 ENDMDL | | | MODEL????9783 REMARK? Name= ZINC000739744108 REMARK? 6active torsions: REMARK?status: ('A' for Active; 'I' for Inactive) REMARK???1? A??? between atoms: C1_1? and?N2_2 REMARK???2? A??? between atoms: C3_3? and?C5_5 REMARK???3? A??? between atoms: C5_5? and?C6_6 REMARK???4? A??? between atoms: N8_8? and?C9_9 REMARK???5? A??? between atoms: C9_9? and?C10_10 REMARK???6? A??? between atoms: C10_10? and?N11_11 REMARK??????????????????????????? x?????? y??????z???? vdW? Elec??????q??? Type REMARK???????????????????????? _______ ______________ _____ _____??? ______ ____ ROOT ATOM?????6? C6? ZIN A??1?????? 0.667? -2.924??0.161? 0.00? 0.00???+0.560 C ATOM?????7? O7? ZIN A??1?????? 1.353? -3.920??0.250? 0.00? 0.00???-0.530 OA ATOM?????8? N8? ZIN A??1????? -0.037? -2.493??1.227? 0.00? 0.00???-0.710 N ATOM????18? H21 ZIN A?? 1?????-0.527? -1.658?? 1.179?0.00? 0.00??? +0.410 HD ENDROOT BRANCH??6?? 5 ATOM?????5? C5? ZIN A??1?????? 0.601? -2.167?-1.140? 0.00? 0.00???-0.200 C ATOM????15? C15 ZIN A?? 1?????-0.616? -2.405? -2.036?0.00? 0.00??? +0.090 C ATOM? ???16?C16 ZIN A?? 1?????? 0.749?-2.971? -2.433? 0.00?0.00??? +0.100 C BRANCH??5?? 3 ATOM?????1? C1? ZIN A??1?????? 3.029?? 0.770?-1.492? 0.00? 0.00???+0.290 C ATOM?????2? N2? ZIN A??1?????? 2.486? -0.588?-1.409? 0.00? 0.00???-0.730 N ATOM?? ???3?C3? ZIN A?? 1??????1.185? -0.778? -1.115?0.00? 0.00??? +0.560 C ATOM?????4? O4? ZIN A??1?????? 0.484?? 0.170?-0.829? 0.00? 0.00???-0.520 OA ATOM????17? H20 ZIN A?? 1??????3.064? -1.351? -1.567?0.00? 0.00??? +0.410 HD ENDBRANCH??5?? 3 ENDBRANCH??6?? 5 BRANCH??8?? 9 ATOM?????9? C9? ZIN A??1????? -0.062? -3.288??2.458? 0.00? 0.00???+0.250 C BRANCH??9? 10 ATOM????10? C10 ZIN A?? 1?????-0.926? -2.581?? 3.504?0.00? 0.00??? +0.230 C BRANCH?10? 11 ATOM????11? N11 ZIN A?? 1?????-0.951? -3.375?? 4.735?0.00? 0.00??? -0.780 N ATOM????12? C12 ZIN A?? 1?????-1.655? -2.945?? 5.800?0.00? 0.00??? +0.660 C ATOM????13? O13 ZIN A?? 1?????-2.273? -1.891?? 5.740?0.00? 0.00??? -0.720 OA ATOM????14? O14 ZIN A?? 1?????-1.675? -3.608?? 6.828?0.00? 0.00??? -0.720 OA ATOM????19? H26 ZIN A?? 1?????-0.460? -4.211?? 4.782?0.00? 0.00??? +0.370 HD ENDBRANCH?10? 11 ENDBRANCH?? 9? 10 ENDBRANCH??8?? 9 TORSDOF 5 ENDMDL ? ? ?????(Note2) Virtual screening run by CYGDRIVEwhich shows error message. ? ? Eiichi Akaho at DESKTOP-EF6R6S2 /cygdrive/c/my_document/vd_1t64_zinc100 $./VS01.bash Processingligand ZINC19aug ############################################################## #If you used AutoDock Vina in your work, please cite:?????? # #???????????????????????????????????????????????????????????# #O. Trott, A. J. Olson,?? ??????????????????????????????????# #AutoDock Vina: improving the speed and accuracy of docking # #with a new scoring function, efficient optimization and??? # #multithreading, Journal of Computational Chemistry (2009)? # #????????????????????????????? ??????????????????????????????# #DOI 10.1002/jcc.21334????????????????????????????????????? # #???????????????????????????????????????????????????????????# #Please see http://vina.scripps.edu for more information.?? # ############################################################## ? Detected2 CPUs Readinginput ... ? Parse error on line 1 in file"ZINC19aug.pdbqt": Unknown or inappropriate tag ? ? ???What Idid as a tentative trial solution (not a completesolution) is as follows **** ? I thought that since the line?1?is ?MODEL?? 1?, Putting REMARK in front might work. It worked, but another error,?Parse error on line 43 infile "ZINC19aug.pdbqt": Unknown or inappropriate tag? appeared. Then? again sinceline?43?is ?ENDMOL?, Putting REMARK in frontof ?ENDMOL? I thought it might work. It worked, ?but another error,?Parse error on line 44 infile "ZINC19aug.pdbqt": Unknown or inappropriate tag? appeared.Unfortunately line 44 is ?MODEL 2?. Therefore, this is just a tentative trialsolution (not a complete solution). Since I have 9873 ZINC pdbqt molecules, youknow that my trial solution is not a perfect solution. Please advise me how tosolve this problem satisfactorily. ? ? ? ??????Note 3?VS01.bash?file ? ? 1.?for f in ZINC*.pdbqt; do? b=`basename $f .pdbqt`; echo Processingligand $b; mkdir -p data01; ./Vina/vina --config conf.txt --ligand $f --outdata01/$f.pdbqt --log data01/$f.txt; done 2.?#result analysis 3.?cd data01 4.?grep "?? 1 " *.txt | cut -c1-12,35-42>>result 5.?cat result ? ?????(Note 4) Conf.txt file ? receptor = 1t64_lg_lock.pdbqt ? center_x = 65.825 center_y = 77.714 center_z = 0.682 ? size_x = 60 size_y = 60 size_z = 60 ? num_modes = 10 ? ? ? Thank you very much for your help in advance. ? Sincerely yours, ? Eiichi From horse16031603 at yahoo.co.jp Sat Sep 26 00:00:38 2020 From: horse16031603 at yahoo.co.jp (horse16031603 at yahoo.co.jp) Date: Sat, 26 Sep 2020 16:00:38 +0900 (JST) Subject: ADL: virtual screening References: <1743057045.459154.1601103639132.JavaMail.yahoo.ref@mail.yahoo.co.jp> Message-ID: <1743057045.459154.1601103639132.JavaMail.yahoo@mail.yahoo.co.jp> Hi honorable AutoDockers: I have done a virtual screening successfully as in the attached my paper (VSDK.pdf).However, in this way, I had to save a ZINC PDBQT small molecule, individually, that is, one by one, whichtakes a lot of time.? So, I downloaded 9783 ZINC 3D PDBQT molecules all at once as one file and didvirtual screening by the same way in my paper. But this time the errors showed up,? It seems that the Bash script seems to be modified. If anyone knows how to modify the Bash file in the paper, I appreciate it very much.?? Thank you very much for your help in advance.Eiiichi -------------- next part -------------- A non-text attachment was scrubbed... Name: VSDK.pdf Type: application/pdf Size: 122895 bytes Desc: not available URL: From sherif.elsabbagh at hotmail.com Sat Sep 26 01:46:04 2020 From: sherif.elsabbagh at hotmail.com (Sherif Arafa) Date: Sat, 26 Sep 2020 08:46:04 +0000 Subject: ADL: Split molecule not working Message-ID: Dear AD users I have a protein molecule with a ligand and I want to split the ligand from the protein so I can dock another ligands. I select the ligand, choose split molecule as protein and then there is an error and the programme stops working. This happened with many complexes. So what can i do ? Sherif Elsabbagh PhD Candidate Institute of Pharmacy University of Tuebingen 72076, Heuberger Tor Weg 15, Tuebingen From amr_alhossary at hotmail.com Sat Sep 26 01:52:44 2020 From: amr_alhossary at hotmail.com (Amr ALHOSSARY) Date: Sat, 26 Sep 2020 08:52:44 +0000 Subject: ADL: Split molecule not working In-Reply-To: References: Message-ID: Dear Sherif, I recommend using another tool to do this task. One good example is pyMol, where you can select the molecules / residues you want, and save them separately with ease. Another good tool is UCSD Chimera. Regards Amr Amr Ali Mokhtar ALHOSSARY MBBS, PhD Research Fellow, Rehabilitation Research Institute of Singapore (RRIS), Nanyang Technological University 11 Mandalay Road #14-03, Clinical Sciences Building, Singapore 308232. T +65 6904-1355 | M +65-9457-2816 | E? aalhossary at ntu.edu.sg| Web www.rris.ntu.edu.sg ? -----Original Message----- From: autodock-bounces at scripps.edu On Behalf Of Sherif Arafa Sent: Saturday, September 26, 2020 4:46 PM To: autodock at scripps.edu Subject: ADL: Split molecule not working Dear AD users I have a protein molecule with a ligand and I want to split the ligand from the protein so I can dock another ligands. I select the ligand, choose split molecule as protein and then there is an error and the programme stops working. This happened with many complexes. So what can i do ? Sherif Elsabbagh PhD Candidate Institute of Pharmacy University of Tuebingen 72076, Heuberger Tor Weg 15, Tuebingen ________________________________________________ --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list --- From bsaman4 at uic.edu Sat Sep 26 15:31:03 2020 From: bsaman4 at uic.edu (Banafshe Samani-Ghaleh-Taki) Date: Sat, 26 Sep 2020 17:31:03 -0500 Subject: ADL: Error in ligand Message-ID: Hello, I am pretty new to Autodock, I installed the program and after I prepared the ligand and protein I pressed Run, Run AutoGrid. But I saw an error message. Please help me. the error message is : ERROR ********************************************* Traceback (most recent call last): File "/Library/MGLTools/1.5.6/MGLToolsPckgs/ViewerFramework/VF.py", line 898, in tryto result = command( *args, **kw ) File "/Library/MGLTools/1.5.6/MGLToolsPckgs/AutoDockTools/autostartCommands.py", line 964, in doit ps = subprocess.Popen(args) File "/Library/MGLTools/1.5.6/lib/python2.5/subprocess.py", line 594, in __init__ errread, errwrite) File "/Library/MGLTools/1.5.6/lib/python2.5/subprocess.py", line 1097, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory Thank you, Banafshe