[Dock-fans] help request about making mol2 files for dock

Trent E. Balius tbalius at aol.com
Wed Apr 11 19:19:05 PDT 2012




 Hi Gaurav,

The amber99sb force field is for proteins.
  
GAFF is a force field for small molecules, but does not have a charge component.  
  
Charges for small molecules are typically assigned using a quantum mechanical calculation (AM1-BCC for example).
  
Mol2 files usually use sybyl atom types (http://tripos.com/mol2/atom_types.html).  
        
DOCK internally applies an amber force field for the van der Waals radii using the sybyl atom types and environment.
Charges are read in from the mol2 file.  
        
I will investigate the molecule you sent and get back to you.  

You may wish to add Gasteiger charges which are very easy to calculate but are not as realistic as AM1-BCC.
        
Hope this helps,
 

Trent E. Balius
Graduate Student, Rizzo Group
Department of Applied Mathematics and Statistics,
Stony Brook University.
Office: Math Tower 3-129, Phone: (631) 632-8519
URL: http://www.ams.sunysb.edu/~tbalius/

 

 

-----Original Message-----
From: Gaurav Chopra <gaurav at compbio.washington.edu>
To: Trent E. Balius <tbalius at aol.com>
Cc: dock-fans <dock-fans at docking.org>; jir322 <jir322 at gmail.com>; rizzorc <rizzorc at gmail.com>; sudipto.mukherjee <sudipto.mukherjee at gmail.com>; william.joseph.allen <william.joseph.allen at gmail.com>; jianglilian68 <jianglilian68 at gmail.com>; brianfochtman <brianfochtman at gmail.com>; yulinhuang2007 <yulinhuang2007 at gmail.com>
Sent: Wed, Apr 11, 2012 5:46 pm
Subject: Re: help request about making mol2 files for dock


Dear Trent,


Thank you so much for your reply. I am using chimera v.1.6.1 and a lot of the fda approved small molecules fail. I am attaching a mol file for one such case (working.mol file attached). It would be great if you can look into it and let me know if you can get this to working to write out mol2 using antechamber (amber99sb force field).


Also, I wanted to ask that do we have support for GAFF method from antechamber to assign charges in chimera?


Do you think I should try with the antechamber in the Amber software. I do not have the latest version though. I think I only have Amber 9 which may not be better than what is already in Chimera?


Best,
Gaurav


On Wed, Apr 11, 2012 at 9:52 AM, Trent E. Balius <tbalius at aol.com> wrote:

 Hi Gaurav,  

How many molecules fail, all 4000?

Chimera calls antechamber which is part of Amber tools.  SQM is the module that antechamber runs to perform semi-empirical quantum mechanical charge (AM1-BCC) calculations.

Sometimes SQM does not converge.  see the following postings to Amber mailing list.

http://dev-archive.ambermd.org/201101/0063.html
http://archive.ambermd.org/201201/0197.html

Older versions of antechamber used MOPAC for charge calculations.  If you get an earlier version of Chimera that uses MOPAC you may not have these convergence issues. 

Amber 12 was just released.  I don't know if some of these issues were resolved?

Trent E. Balius
Graduate Student, Rizzo Group
Department of Applied Mathematics and Statistics,
Stony Brook University.
Office: Math Tower 3-129, Phone: (631) 632-8519
URL: http://www.ams.sunysb.edu/~tbalius/


-----Original Message-----
From: Robert C. Rizzo <rizzorc at gmail.com>
To: jir322 <jir322 at gmail.com>
Cc: Trent Balius <tbalius at ams.sunysb.edu>; Sudipto Mukherjee <sudipto.mukherjee at gmail.com>; Joe Allen <william.joseph.allen at gmail.com>; Lingling Jiang <jianglilian68 at gmail.com>; Brian Fochtman <brianfochtman at gmail.com>; Yulin Huang <yulinhuang2007 at gmail.com>
Sent: Wed, Apr 11, 2012 12:13 pm
Subject: Re: help request about making mol2 files for dock


Hi John,

Nice to hear from you.  No problem, I'll have a student contact Gaurav for help.

Dear group please see email below.  Can someone please contact them
for help.  Maybe we want to have this posted in DOCK fans so everyone
can get the benefit of your response.

Thanks -Rob

Robert C. Rizzo, Ph.D., Associate Professor
Department of Applied Mathematics and Statistics,
Institute of Chemical Biology & Drug Discovery,
Laufer Center for Physical & Quantitative Biology
Stony Brook University
Stony Brook NY, 11794-3600
Cell: (631) 944-2891
Office: (631) 632-9340
Fax: (631) 632-8490
rizzorc at gmail.com
http://www.ams.sunysb.edu/~rizzo



On Wed, Apr 11, 2012 at 11:05 AM, John Irwin <jir322 at gmail.com> wrote:
> Hi Rob
>
> Can you forward to group members who might help this person?
>
> Hope all goes well.
>
> Thanks
>
> John
>
>
>
> ---------- Forwarded message ----------
> From: Gaurav Chopra <gaurav at compbio.washington.edu>
> Date: Wed, Apr 11, 2012 at 2:19 AM
> Subject: help request about making mol2 files for dock
> To: jji at cgl.ucsf.edu












>
>
> Dear John,
>
> My name is Gaurav Chopra and I am a postdoc with Professor Michael
> Levitt at Stanford University and Professor Ram Samudrala at
> University of Washington. I have been trying to benchmark dock6
> against my docking method using all FDA approved small molecule
> compounds and I am faced with a small hurdle.
>
> When I try to convert the mol files to mol2 in chimera and give them
> charges using antechamber it fails and gives an error shown at the end
> of this email within "===". I  was wondering if you would be so kind
> to help me in this matter. For one of the drugs which does not work
> (attached mol2 file) with antechamber (amber99sb force field) it would
> be great if you could guide me how to proceed or if you have an
> automated script which I can use to do this for my dataset of ~4000
> compounds. The net charge of the molecule is 0 and hydrogens are
> already present in the mol file but can be added again. I have been
> using the dockprep module in chimera to do this but it is not working
> no matter what changes I make.
>
> To run with DOCK6  I need a mol2 file and thus I am seeking your help.
>
> On a different note, I wanted to ask you if it is possible to get the
> version of the docking program which you use in your group (which I
> know is different from the source code branch of 3.x and very
> different than v. 6.5). I would be perfectly fine with the
> executable(s) if the source is proprietary. Like i said this is really
> needed for benchmarking purposes and depending on the results I would
> include it into my docking pipeline which is a flexible docking
> pipeline with sampling done in torsional space with a knowledge-based
> potential.
>
> Please let me know what do you think.
>
> Best,
> Gaurav
>
>
> === ERROR ===
> Running ANTECHAMBER command:
> /tmp_mnt/cosmos/das/home/ambrish/bin/chimera/bin/amber11/bin/antechamber
> -ek qm_theory='AM1', -i /tmp/tmpamfdkm/ante.in.mol2 -fi mol2 -o
> /tmp/tmpamfdkm/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2
>
> Error while processing lig_prep.py:
> Failure running ANTECHAMBER for residue UNK
> Check reply log for details
> 1:19 AM
> No incomplete side chains
>
> Chain-initial residues that are actual N terminii:
>
> Chain-initial residues that are not actual N terminii:
>
> Chain-final residues that are actual C terminii:
>
> Chain-final residues that are not actual C terminii:
>
> 0 hydrogen bonds
>
> Hydrogens added
>
> Charge model: AMBER ff99SB
>
> Assigning partial charges to residue UNK (net charge +0) with am1-bcc method
>
> Running ANTECHAMBER command:
> /tmp_mnt/cosmos/das/home/ambrish/bin/chimera/bin/amber11/bin/antechamber
> -ek qm_theory='AM1', -i /tmp/tmpamfdkm/ante.in.mol2 -fi mol2 -o
> /tmp/tmpamfdkm/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2
>
> Error while processing lig_prep.py:
> Failure running ANTECHAMBER for residue UNK
> Check reply log for details
>
> ========
>
>
> --
> Gaurav Chopra, Ph.D.
>
> Levitt Group, Clark S255
> Department of Structural Biology
> Stanford University - School of Medicine
> Phone: (650) 723-5720
> Fax: (650) 723-8464
> http://www.stanford.edu/~gauravc
>
> Samudrala Group
> Department of Microbiology
> University of Washington - School of Medicine
> http://cando.compbio.washington.edu/
>
> Mobile: (650) 283-2192













 






-- 

Gaurav Chopra, Ph.D.


Levitt Group, Clark S255
Department of Structural Biology
Stanford University - School of Medicine
Phone: (650) 723-5720
Fax: (650) 723-8464
http://www.stanford.edu/~gauravc





Samudrala Group
Department of Microbiology
University of Washington - School of Medicine
http://cando.compbio.washington.edu/


Mobile: (650) 283-2192


 
 
 
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