ADL: autodock Digest, Vol 43, Issue 13

jose correa corrjose at gmail.com
Thu Oct 11 13:02:51 PDT 2007


Dear Bagaria
I had the same problen because at pH=7, such residues that you mention must
be total charges according to my elemental biochemistry. Then, I used the
protein with and with protonation and the results showed very different. But
I dot not know, what is the metho more safe?.


2007/10/12, autodock-request at scripps.edu <autodock-request at scripps.edu>:
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> Today's Topics:
>
>   1.  protein-protein docking (Zheng Cai)
>   2.  Setting the grid over specific residues (Lokesh P. Tripathi)
>   3.  fragmental volume and solvation parameters (ANURAG BAGARIA)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 10 Oct 2007 16:08:37 -0400
> From: Zheng Cai <zhengcai at mail.med.upenn.edu>
> Subject: ADL: protein-protein docking
> To: autodock at scripps.edu
> Message-ID: <1192046917.470d3145b0895 at webmail.pobox.upenn.edu>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi everybody,
>
> I am trying to do a protein-protein docking using autoDock4. I wonder if
> you
> ever had any successful experience with the similar project? I would
> greatly
> appreciate if you could kindly share any info about that.
>
> Thanks~
> David
> --
> Zheng Cai, Ph.D.
> Department of Pathology and Laboratory Medicine
> University of Pennsylvania School of Medicine
> 252 John Morgan Building
> 36th Street and Hamilton Walk
> Philadelphia, PA 19104
> (lab-tel) 215-898-2870
>
>
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 11 Oct 2007 12:10:56 +0530 (IST)
> From: "Lokesh P. Tripathi" <lokesh at ncbs.res.in>
> Subject: ADL: Setting the grid over specific residues
> To: autodock at scripps.edu
> Message-ID: <45398.192.168.1.1.1192084856.squirrel at mail.ncbs.res.in>
> Content-Type: text/plain;charset=iso-8859-1
>
> Dear all
>
> I am using autodock 3.05 to perform the docking of a tryptase inhibitor
> (41 amino acids in length) to a trypsin structure (native PDB stucture and
> a modeller derived homology model). I have faced a few issues in this and
> woudl be extremely grateful if someone could provide some clues on how to
> get around these problems
>
> 1. when I select the macromolecule (for preparation) using
> Grid-macromolecule-Choose...(AG3) command, I get the foloowing message
> initializing xxx.pdb
> it is not a peptide
> -added gasteiger charges
> -found 0 non-polar hydrogens
> -added solvation parameters
>
> I am not sure about the message it is not peptide. Is it because the
> protein in question is over 200 residues long and so technically doesn't
> qualify as a peptide? But the protein provided for test purposes too
> contains 100 residues and is identified as a peptide by Autodock. Is there
> any particular input format prior to preparing the PDB file by adding
> hydrogens?
>
> 2. That brings me to the next question. The file was genrated by splitting
> a PDB complex into two PDB files using a text editor and thus, the two new
> PDB files retain only the ATOM record for either protein. Wil this cause
> any problems with autodock (such as above)?
>
> 3. The most imposratnt part. I wish to bind the inhibitor (ligand) to
> enzyme active site by placing thr GRID Over the binding site region
> demarcated by a set of residues say 189-192, 214-216 and 224-228. How can
> I do that using ADT or through command line?
>
> Any assistance would be most welcome
>
> Lokesh P. Tripathi
> National Centre for Biological Sciences,
> Bangalore, India
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 11 Oct 2007 05:21:48 -0700
> From: "ANURAG BAGARIA" <anurag.bagaria at gmail.com>
> Subject: ADL: fragmental volume and solvation parameters
> To: autodock at scripps.edu
> Message-ID:
>        <e2ea20840710110521y18ef1163m47760595fac2a990 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> With reference to a previous post (more than 3 years back) at :
>
> http://mgldev.scripps.edu/cgi-bin/perlfect/search/search.pl?q=solvation%20parameter&showurl=%2Fautodock%2F2004-May%2F000105.html
>
> Dear Autodockers,
>
>
>
> Is there any web server or stand alone software (Free of cost)
>
> available for the converstion of PDB formated macromolecule to PDBQ
> formated one reliably ?
>
> if no such softwares, please give me the formula or methodology to
> calculate these atomic
>
> solvation parameter , so I can manually calculate and edit in my PDBQS
> file.I am asking this question due to the following problem I
> faced....
>
> 1)I tried BABEL program to convert PDB(macromolecule) into mol2, then
> into pdbq using 'mol2topdbq' program, then added atomic solvation
> arameter by 'addsol' parameter but the resulted pdbqs file contains
> value of '0' in all fields of coluim number 71 to 76 .What's going
> wrong here?
>
> 2) I still attempted to use that pdbqs file for further docking study
> and got somehow favaourable result...I am wondering now, whether the
> positiveresult that I got purely by fluke....otherwise it is the power
> of autodock to perform correct docking without atomic solvation
> parameter..!
>
> 3) Earlier, while using autogrid,the program itself enabled the -o
> flag in grid calculation due to the average value of 0 found at 71 to
> 76 col of the PDBQS file, Please correct me if I am wrong at anywhere
> in the format converstion methodology....I don't have commercial
> softwares such as InsightII,SYBYL..at this moment etc...
>
> Yours truly,
>
> B.Nataraj
>
>
>
> B.Nataraj,
> Final year M.Tech.(Bioinformatics),
> SASTRA Deemed University,
> (www.sastra.edu)
> Thanjavur,
> Tamil Nadu,
> India.
> Email:nataraj at biotech2.sastra.edu
> <http://mgldev.scripps.edu/mailman/listinfo/autodock>
> Email:natarajmtech at yahoo.co.uk
> <http://mgldev.scripps.edu/mailman/listinfo/autodock>
>
>
> I would like to inform that I too did face a similar problem and finally
> ended up editing the q.kollua file so as to include some more residue
> types
> (in a different protonation stage) by referring to the Xleap program and
> reading about the protonation stages of different residues. But now when
> coming to the solvation parameters file I am unable to find the
> corresponding values and am stuck up at this point.
>
> Can someone please provide me with some information with regard to
> residues
> ASH and GLH (neutral ASP and GLU respectively). I would be very thankful
> to
> the concerned person.
> --
>
>
>
> ANURAG KUMAR BAGARIA
>
>
> ------------------------------
>
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> End of autodock Digest, Vol 43, Issue 13
> ****************************************
>



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