From jonwil6425 at gmail.com  Sun Jan  3 15:44:45 2021
From: jonwil6425 at gmail.com (Jon Wil)
Date: Sun, 3 Jan 2021 23:44:45 +0000
Subject: ADL: Nobel prize winning Potassium cation and 18 crown ether
 complexation and modeling
Message-ID: <CA+B3mfBDjm3Tud4b1DvrXt6XtaoBcq7HLxk0J9TE1zzYPKq8UQ@mail.gmail.com>

Hi folks
I thought I would see how autodock models the properties of Charles
Peddersons discoveries of crown ethers that led him to be awarded the
Nobel prize for Chemistry in 1987:

*[ https://en.wikipedia.org/wiki/Crown_ether
<https://en.wikipedia.org/wiki/Crown_ether> ].*


So to start with  Iwas trying to dock NaOH with 18 C - 6 i.e.,
[image: image.png]
I have download the NaOH 2D sdf file from pubchem and converted it to PDB
in Pymol but when I try to import it as a ligand I get the following error
messages:


*Sodium cation from pubchem Structure2D_CID_923 : :UNK0:Na and Sodium
cation from pubchem Structure2D_CID_923 : :UNK0:Na have the same
coordinatesERROR*


*and*


*forcing addition of gasteiger charges to molecule with all zero charges
 Sorry, there are no Gasteiger parameters available for atom Sodium cation
from pubchem Structure2D_CID_923 : :UNK0:NaSodium cation from pubchem
Structure2D_CID_923 : :UNK0:Na and Sodium cation from pubchem
Structure2D_CID_923 : :UNK0:Na have the same coordinates*


Here is the NaOH  file info:
[image: image.png]

Any ideas? I tried adding  "Gasteiger charges"  but the error messages just
came up again. I am new to Autodock and have searched hard for any info on
this and for cations as ligands in general and how to dock them; for
example by looking in Autodock's manual and the forum etc., to solve this,
but cant find anything.

Many thanks in advance for your help

Kind regards
Jon

From ricksher at gmail.com  Wed Jan  6 00:29:38 2021
From: ricksher at gmail.com (Rick Sheridan)
Date: Wed, 6 Jan 2021 11:29:38 +0300
Subject: ADL: Any literature survey of Vina-in vitro correlations?
Message-ID: <CAEwcKcf6C=mDrChKEieUAbVS6bW4hpHedWOZCE71=yHVGjBPTA@mail.gmail.com>

Hi dockers,

In the years since Vina came out, does anyone know if any researcher has
run a comprehensive survey and correlation comparison of Vina binding
energy results with literature-wide in vitro (cell-free) measured IC50
values in the laboratory?  There was the original DUD-E dataset comparison
when Vina first came out, but I am unfamiliar with work that has built on
that since then.

Best,
Rick
-- 
-- 
********************************************************************
Rick Sheridan
********************************************************************

From drasko.tomic at yahoo.com  Wed Jan  6 06:16:05 2021
From: drasko.tomic at yahoo.com (Drasko Tomic)
Date: Wed, 6 Jan 2021 14:16:05 +0000 (UTC)
Subject: ADL: Any literature survey of Vina-in vitro correlations?
In-Reply-To: <CAEwcKcf6C=mDrChKEieUAbVS6bW4hpHedWOZCE71=yHVGjBPTA@mail.gmail.com>
References: <CAEwcKcf6C=mDrChKEieUAbVS6bW4hpHedWOZCE71=yHVGjBPTA@mail.gmail.com>
Message-ID: <1398173505.5941145.1609942565084@mail.yahoo.com>

 Hi Rick,
hope this may help: https://www.hilarispublisher.com/open-access/evaluation-of-the-efficacy-of-cancer-drugs-by-using-the-second-largest-eigenvalue-of-metabolic-cancer-pathways-jcsb-1000280.pdf
Vina binding results were validated against NCI-60 in vitro results there. 

Regards,
Drasko


    On Wednesday, January 6, 2021, 9:31:17 AM GMT+1, Rick Sheridan <ricksher at gmail.com> wrote:  
 
 Hi dockers,

In the years since Vina came out, does anyone know if any researcher has
run a comprehensive survey and correlation comparison of Vina binding
energy results with literature-wide in vitro (cell-free) measured IC50
values in the laboratory?? There was the original DUD-E dataset comparison
when Vina first came out, but I am unfamiliar with work that has built on
that since then.

Best,
Rick
-- 
-- 
********************************************************************
Rick Sheridan
********************************************************************
________________________________________________
--- ADL: AutoDock List? --- http://autodock.scripps.edu/mailing_list ---
  

From mathilde.goullieux at unil.ch  Fri Jan  8 05:18:16 2021
From: mathilde.goullieux at unil.ch (mgoullie)
Date: Fri, 8 Jan 2021 06:18:16 -0700 (MST)
Subject: ADL: covalent docking with Autodock - RMSD calculation
Message-ID: <1610111896474-0.post@n2.nabble.com>

Hi,

I did some covalent dockings with Autodock, using the flexible side chains
method.
I ran into different problems, because the atoms are renamed, and
re-organised, so it makes it impossible to calculate RMSD values.

Also, in the example given when one downloads the covalent docking tutorial
and script files, the RMSD printed in the output is -nan.

So, how is it possible to get a RMSD value ?

Finally, in the same scripts, a README.txt file is given (I copied its
content at the end of this message), with the instructions for running
covalent docking. In that file, it is written :

"Also, in order to include the ligand atoms in the calculation of RMSD and
clustering, the following parameters need to be added:

    rmsdatoms all
"

but adding this keyword gives the following message :

"autodock4: FATAL ERROR: DPF> rmsdatoms all

autodock4: ERROR: Unrecognized keyword in docking parameter file.

autodock4: Unsuccessful Completion."

so apparently this option does not even exist.

Did someone ran into the same problem as me ? And most important, could
anyone provide a solution ?

All the best,
Mathilde





README.txt file :

This tutorial describes how to apply the 'flexible side chain' covalent
docking as described in the paper:

   "Covalent docking using autodock: Two-point attractor and flexible side
chain methods"
   http://www.ncbi.nlm.nih.gov/pubmed/26103917

If you use this method, please cite the paper.
Happy dockings!

==============
REQUIREMENTS
==============
- Python  >=2.6
- OpenBabel Python bindings
   (On Debian/Ubuntu derivatives, it can be installed with "apt-get install
python-openbabel")

- Basic experience with docking with AutoDock

==============
INSTALLATION
==============
- Copy the directory 'adcovalent' in a location that is accessible from the
user (i.e., '~/local/adcovalent').

==============
USAGE
==============

The preparation code is used to generate the geometry of the ligand
covalently bound to the
residue. Once the ligand initial coordinate is generated, the PDBQT files of
the receptor and
flexible ligand need to be generated using prepare_flexreceptor4.py script
in AutoDockTools.

The directory '3upo_test' contains an example case of a ligand ready to
processed.
The following examples assume a terminal opened in that location.


1. Generate the alignment
--------------------------
The input ligand structure must be modeled with a portion of the alkylated
residue already present,
i.e. for a ligand bound to a serine:

         LIGAND-OG-CB-CA-RESIDUE  [MOL1]

the ligand structure to process should be:

         LIGAND-O-C [MOL2]

where C and O are the two atoms that are going to be used for the alignment.
More in general:

        0. Initial configuration

                    B
                   /
           [L]----A      I---J--[R]
                        /
                       X

        1. Translate [L] to overlap A->I

                    B
                   /
           [L]----A  ->  I---J--[R]
                        /
                       X
                          B
                         /
                 [L]----AI---J--[R]
                        /
                       X

        2. Rotate [L] around the normal of plane (B,A,J) to overlap B->J

                [L]
                  \
                   AI--BJ--[R]
                   /
                  X

The alignment could be skipped if the ligand is already attached to the
receptor structure
(i.e., a re-docking experiment from a PDB is going to be perfoemd).

To perform the alignment, a receptor file and a residue name (Chain:ResNum)
must
be specified, then a ligand file and an alignment criterion.

The ligand alignment can be defined in two ways. The first is by specifying
the atom indices in the ligand file (i.e., first and second atoms):

    python  ~/local/adcovalent/prepareCovalent.py --ligand ligand.mol2 \
                  --ligindices 1,2\
                  --receptor 3upo_protein.pdb\
                  --residue B:SER222\
                  --outputfile ligcovalent.pdb

2. Generate PDBQT files
--------------------------
The standard PDBQT files for AutoDock need to be generated for both the
receptor structure. The standard ADT scripts
are going to be used, assuming that $MGLROOT is the path where ADT has been
installed.

*** NOTE: if a covalent ligand is already bound to the residue in the
protein structure, it must be removed! ***

    $MGLROOT/bin/pythonsh
$MGLROOT/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py -r
3upo_protein.pdb -A hydrogens
       [ this generates the file "3upo_protein.pdbqt" ]

and the covalent ligand that has been aligned:

    $MGLROOT/bin/pythonsh
$MGLROOT/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py -r
ligcovalent.pdb
       [ this generates the file "ligcovalent.pdbqt" ]


3. Generate flexible/rigid PDBQT files
---------------------------------------
The PDBQT files are going to be used to generate the rigid and flexible
components that are going to be used
for the docking.
First, the receptor is processed to extract the rigid part by specifying
which residue is going to be made flexible:

    $MGLROOT/bin/pythonsh
$MGLROOT/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_flexreceptor4.py -r
3upo_protein.pdbqt -s 3upo_protein:B:SER222
       [ this generates the files "3upo_protein_rigid.pdbqt" and 
"3upo_protein_flex.pdbqt" ]

The same thing is going to be done for the processed ligand:

    $MGLROOT/bin/pythonsh
$MGLROOT/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_flexreceptor4.py -r
ligcovalent.pdbqt -s ligcovalent:B:SER222
       [ this generates the files "ligcovalent_rigid.pdbqt" and 
"ligcovalent_flex.pdbqt" ]

NOTE: if the ligand has not been prepared in step 1, make sure that all
atoms in the ligand have the poper residue id
corresponding to the residue modified (i.e., Ser222A).


4. Generate GPF and DPF files
------------------------------
The parameter files for the actual calculation are going to be generated.
The GPF for AutoGrid is generated with:
    $MGLROOT/bin/pythonsh
$MGLROOT/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_gpf4.py -r
3upo_protein_rigid.pdbqt\
                -x ligcovalent_flex.pdbqt\
                -l ligcovalent_flex.pdbqt\
                -y -I 20\
                -o 3upo_priotein.gpf

The DPF for AutoDock is generated with:

    $MGLROOT/bin/pythonsh
$MGLROOT/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_dpf4.py -r
3upo_protein_rigid.pdbqt\
                -x ligcovalent_flex.pdbqt\
                -l ligcovalent_flex.pdbqt\
                -o ligcovalent_3upo_protein.dpf\
                -p move='empty'

This command instructs the script to dock the covalent ligand as a flexible
residue and ignore any 'true' ligand ("move='empty'"). To do this,
an empty file must be created, and it can be done with the following Unix
command:

    touch empty

Also, in order to include the ligand atoms in the calculation of RMSD and
clustering, the following parameters need to be added:

    rmsdatoms all

which will include flexible residue (and ligand) atoms in the RMSD
calculation.
 Finally, the DPF file must be manually edited to set the appropriate energy
model so that the docking score corresponds to the interaction between
the flexible residue (the ligand) and the rigid receptor. For this, the
entry:

    unbound_model bound

must be replaced with:

    unbound_energy 0.0


5. Run AutoGrid and AutoDock
------------------------------
Both programs can be executed using the standard procedure:

    autogrid4 -p 3upo_priotein.gpf -l 3upo_priotein.glg
    autodock4 -p ligcovalent_3upo_protein.dpf -l 
ligcovalent_3upo_protein.dlg



The output generated at each step of the process is available in the
directory '3upo_test/output'.




--
Sent from: http://autodock.1369657.n2.nabble.com/



From hello at zacharyrs.me  Mon Jan 11 13:47:50 2021
From: hello at zacharyrs.me (Zachary Riedlshah)
Date: Tue, 12 Jan 2021 10:47:50 +1300
Subject: ADL: Segmentation in AutoGrid4 on Ubuntu 20.04.1
Message-ID: <176f36b64b3.fc0864c5224669.3086007154180754202@zacharyrs.me>

Hey all,

Likely a follow on from http://mgldev.scripps.edu/pipermail/autodock/2020-October/011651.html.

I took a look at the core dump and found this:
    __GI__IO_fputs (str=0x128a2ca8 "<path/to/>autogrid4: FATAL ERROR: cannot obtain new fd to concatenate log file\n", fp=0x0) at iofputs.c:33

Unfortunately, I can't get much further as I'm using ADFRsuite which has AutoGrid 4.2.7.x-2019-07-11.
Would I be able to recompile and use 4.2.6 or is there significant difference?

Just wondering how to proceed.

Thanks,
Zach


From hemapriyakumarhp at gmail.com  Mon Jan 11 22:12:56 2021
From: hemapriyakumarhp at gmail.com (Hemapriya Kumar)
Date: Tue, 12 Jan 2021 11:42:56 +0530
Subject: ADL: (no subject)
Message-ID: <CAN9LBWtBwRgeq_aYSZAx9AWiDMZfELU4VtQtNTB0JusVNNkyaw@mail.gmail.com>

While registering mgl tools,  it's coming registration failed,  how to
solve this?

--
With Regards Hemapriya Kumar

From mathilde.goullieux at unil.ch  Mon Jan 11 23:57:32 2021
From: mathilde.goullieux at unil.ch (mgoullie)
Date: Tue, 12 Jan 2021 00:57:32 -0700 (MST)
Subject: ADL: covalent docking with Autodock - RMSD calculation
Message-ID: <1610438252382-0.post@n2.nabble.com>

Hi,

I did some covalent dockings with Autodock, using the flexible side chains
method.
I ran into different problems, because the atoms are renamed, and
re-organised, so it makes it impossible to calculate RMSD values.

Also, in the example given when one downloads the covalent docking tutorial
and script files, the RMSD printed in the output is -nan.

So, how is it possible to get a RMSD value ?

Finally, in the same scripts, a README.txt file is given (I copied its
content at the end of this message), with the instructions for running
covalent docking. In that file, it is written :

"Also, in order to include the ligand atoms in the calculation of RMSD and
clustering, the following parameters need to be added:

    rmsdatoms all
"

but adding this keyword gives the following message :

"autodock4: FATAL ERROR: DPF> rmsdatoms all

autodock4: ERROR: Unrecognized keyword in docking parameter file.

autodock4: Unsuccessful Completion."

so apparently this option does not even exist.

Did someone ran into the same problem as me ? And most important, could
anyone provide a solution ?

All the best,
Mathilde







README.txt file :

This tutorial describes how to apply the 'flexible side chain' covalent
docking as described in the paper:

   "Covalent docking using autodock: Two-point attractor and flexible side
chain methods"
   http://www.ncbi.nlm.nih.gov/pubmed/26103917

If you use this method, please cite the paper.
Happy dockings!

==============
REQUIREMENTS
==============
- Python  >=2.6
- OpenBabel Python bindings
   (On Debian/Ubuntu derivatives, it can be installed with "apt-get install
python-openbabel")
- Basic experience with docking with AutoDock

==============
INSTALLATION
==============
- Copy the directory 'adcovalent' in a location that is accessible from the
user (i.e., '~/local/adcovalent').

==============
USAGE
==============

The preparation code is used to generate the geometry of the ligand
covalently bound to the
residue. Once the ligand initial coordinate is generated, the PDBQT files of
the receptor and
flexible ligand need to be generated using prepare_flexreceptor4.py script
in AutoDockTools.

The directory '3upo_test' contains an example case of a ligand ready to
processed.
The following examples assume a terminal opened in that location.


1. Generate the alignment
--------------------------
The input ligand structure must be modeled with a portion of the alkylated
residue already present,
i.e. for a ligand bound to a serine:

         LIGAND-OG-CB-CA-RESIDUE  [MOL1]

the ligand structure to process should be:

         LIGAND-O-C [MOL2]

where C and O are the two atoms that are going to be used for the alignment.
More in general:

        0. Initial configuration

                    B
                   /
           [L]----A      I---J--[R]
                        /
                       X

        1. Translate [L] to overlap A->I

                    B
                   /
           [L]----A  ->  I---J--[R]
                        /
                       X

                          B
                         /
                 [L]----AI---J--[R]
                        /
                       X

        2. Rotate [L] around the normal of plane (B,A,J) to overlap B->J

                [L]
                  \
                   AI--BJ--[R]
                   /
                  X

The alignment could be skipped if the ligand is already attached to the
receptor structure
(i.e., a re-docking experiment from a PDB is going to be perfoemd).

To perform the alignment, a receptor file and a residue name (Chain:ResNum)
must
be specified, then a ligand file and an alignment criterion.

The ligand alignment can be defined in two ways. The first is by specifying
the atom indices in the ligand file (i.e., first and second atoms):

    python  ~/local/adcovalent/prepareCovalent.py --ligand ligand.mol2 \
                  --ligindices 1,2\
                  --receptor 3upo_protein.pdb\
                  --residue B:SER222\
                  --outputfile ligcovalent.pdb

2. Generate PDBQT files
--------------------------
The standard PDBQT files for AutoDock need to be generated for both the
receptor structure. The standard ADT scripts
are going to be used, assuming that $MGLROOT is the path where ADT has been
installed.

*** NOTE: if a covalent ligand is already bound to the residue in the
protein structure, it must be removed! ***

    $MGLROOT/bin/pythonsh
$MGLROOT/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py -r
3upo_protein.pdb -A hydrogens
       [ this generates the file "3upo_protein.pdbqt" ]

and the covalent ligand that has been aligned:

    $MGLROOT/bin/pythonsh
$MGLROOT/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py -r
ligcovalent.pdb
       [ this generates the file "ligcovalent.pdbqt" ]


3. Generate flexible/rigid PDBQT files
---------------------------------------
The PDBQT files are going to be used to generate the rigid and flexible
components that are going to be used
for the docking.
First, the receptor is processed to extract the rigid part by specifying
which residue is going to be made flexible:

    $MGLROOT/bin/pythonsh
$MGLROOT/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_flexreceptor4.py -r
3upo_protein.pdbqt -s 3upo_protein:B:SER222
       [ this generates the files "3upo_protein_rigid.pdbqt" and 
"3upo_protein_flex.pdbqt" ]

The same thing is going to be done for the processed ligand:

    $MGLROOT/bin/pythonsh
$MGLROOT/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_flexreceptor4.py -r
ligcovalent.pdbqt -s ligcovalent:B:SER222
       [ this generates the files "ligcovalent_rigid.pdbqt" and 
"ligcovalent_flex.pdbqt" ]

NOTE: if the ligand has not been prepared in step 1, make sure that all
atoms in the ligand have the poper residue id
corresponding to the residue modified (i.e., Ser222A).


4. Generate GPF and DPF files
------------------------------
The parameter files for the actual calculation are going to be generated.
The GPF for AutoGrid is generated with:
    $MGLROOT/bin/pythonsh
$MGLROOT/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_gpf4.py -r
3upo_protein_rigid.pdbqt\
                -x ligcovalent_flex.pdbqt\
                -l ligcovalent_flex.pdbqt\
                -y -I 20\
                -o 3upo_priotein.gpf

The DPF for AutoDock is generated with:

    $MGLROOT/bin/pythonsh
$MGLROOT/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_dpf4.py -r
3upo_protein_rigid.pdbqt\
                -x ligcovalent_flex.pdbqt\
                -l ligcovalent_flex.pdbqt\
                -o ligcovalent_3upo_protein.dpf\
                -p move='empty'

This command instructs the script to dock the covalent ligand as a flexible
residue and ignore any 'true' ligand ("move='empty'"). To do this,
an empty file must be created, and it can be done with the following Unix
command:

    touch empty

Also, in order to include the ligand atoms in the calculation of RMSD and
clustering, the following parameters need to be added:

    rmsdatoms all

which will include flexible residue (and ligand) atoms in the RMSD
calculation.
 Finally, the DPF file must be manually edited to set the appropriate energy
model so that the docking score corresponds to the interaction between
the flexible residue (the ligand) and the rigid receptor. For this, the
entry:

    unbound_model bound

must be replaced with:

    unbound_energy 0.0


5. Run AutoGrid and AutoDock
------------------------------
Both programs can be executed using the standard procedure:

    autogrid4 -p 3upo_priotein.gpf -l 3upo_priotein.glg
    autodock4 -p ligcovalent_3upo_protein.dpf -l 
ligcovalent_3upo_protein.dlg



The output generated at each step of the process is available in the
directory '3upo_test/output'.



--
Sent from: http://autodock.1369657.n2.nabble.com/



From hemapriyakumarhp at gmail.com  Tue Jan 12 06:08:55 2021
From: hemapriyakumarhp at gmail.com (Hemapriya Kumar)
Date: Tue, 12 Jan 2021 19:38:55 +0530
Subject: ADL: (no subject)
Message-ID: <CAN9LBWuvPJ=3jXOaNjpa8=cPhBS_r5opzvPNQCiKwAn8K_T19g@mail.gmail.com>

How to register at mgltools registration , for me , it's getting like
registration failed

--
With Regards
Hemapriya Kumar

From 20201023005 at stu.scau.edu.cn  Tue Jan 12 18:46:05 2021
From: 20201023005 at stu.scau.edu.cn (=?UTF-8?B?5a6L56Wl5rCR?=)
Date: Wed, 13 Jan 2021 10:46:05 +0800 (GMT+08:00)
Subject: ADL: autodock download link
Message-ID: <db29bdd.24be.176f9a2ced4.Coremail.20201023005@stu.scau.edu.cn>

Can I request a download link for autodock? Thank you very much, I have completed the registration before this.

From hemapriyakumarhp at gmail.com  Tue Jan 12 23:56:31 2021
From: hemapriyakumarhp at gmail.com (Hemapriya Kumar)
Date: Wed, 13 Jan 2021 13:26:31 +0530
Subject: ADL: autodock download link
In-Reply-To: <db29bdd.24be.176f9a2ced4.Coremail.20201023005@stu.scau.edu.cn>
References: <db29bdd.24be.176f9a2ced4.Coremail.20201023005@stu.scau.edu.cn>
Message-ID: <CAN9LBWv+LyKZ8NR7_cdow0kVu45ODLnQeKf-CCQDFdC+Z_fXBA@mail.gmail.com>

How to register for mgl tools registration

--
With Regards Hemapriya Kumar

On Wed, 13 Jan 2021, 8:25 am ???, <20201023005 at stu.scau.edu.cn> wrote:

> Can I request a download link for autodock? Thank you very much, I have
> completed the registration before this.
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
>

From sanner at scripps.edu  Tue Jan 19 11:58:26 2021
From: sanner at scripps.edu (Michel Sanner)
Date: Tue, 19 Jan 2021 19:58:26 +0000
Subject: ADL: (no subject)
Message-ID: <A453AAF0-4D9D-4644-AD39-1A1B13407AE2@scripps.edu>

I am sorry about this I will look into it

From: <autodock-bounces at scripps.edu> on behalf of Hemapriya Kumar <hemapriyakumarhp at gmail.com>
Reply-To: "autodock at scripps.edu" <autodock at scripps.edu>
Date: Monday, January 11, 2021 at 10:13 PM
To: "autodock at scripps.edu" <autodock at scripps.edu>
Subject: ADL: (no subject)

While registering mgl tools,  it's coming registration failed,  how to
solve this?

--
With Regards Hemapriya Kumar
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---


From tgillyard at mmc.edu  Tue Jan 19 22:10:03 2021
From: tgillyard at mmc.edu (Gillyard, Taneisha R.)
Date: Wed, 20 Jan 2021 06:10:03 +0000
Subject: ADL: Error when running Autodock Vina from AutoDock Tools
Message-ID: <BL0PR18MB2292C9F04F29B0FFFCF8CE1EB7A21@BL0PR18MB2292.namprd18.prod.outlook.com>

Hello,

I am attempting to run AutoDock Vina straight from AutoDock tools after preparing and loading my receptor and ligand files.

I keep getting the following error:
Command line parse error: too many positional options

I'm fairly new to this but I haven't had issues before. I went back and tried it again with a receptor and ligand file I was able to complete successfully and it is still giving me the same error.

Any advice would be appreciated.

Thank you!

TC