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

Scott Brozell sbrozell at rci.rutgers.edu
Thu Apr 12 00:59:19 PDT 2012


Hi,

You could download and install AmberTools 12.
Then execute the antechamber command in the Chimera error message, eg,

/amber12/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

fixing the paths as necessary.

scott

On Thu, Apr 12, 2012 at 12:28:55AM -0700, Gaurav Chopra wrote:
> Hi Scott and Trent,
> 
> Just a clarification that the problem only arises when I ask for generation
> of charges (using AM1-BCC or Gasteiger - I have to check the Gasteiger
> charges part again). Ofcourse, when zero charges are requested the mol2
> file conversion happens without any problems.
> 
> If there is something I can do to generate the antechamber error which can
> be used for diagnosis please let me know.
> 
> Thanks so much for help.
> 
> Best,
> Gaurav
> 
> On Thu, Apr 12, 2012 at 12:13 AM, Scott Brozell <sbrozell at rci.rutgers.edu>wrote:
> 
> > Hi,
> >
> > I am surprised that
> > 'a lot of the fda approved small molecules fail.'
> > Unfortunately, the error message below does not provide the detailed
> > error output from antechamber that could be used for diagnosis.
> > A search of the Amber reflector http://ambermd.org/#reflector
> > does not find any hits for fda approved or similar,
> > so we shall have to wait for Trent's investigation
> > (or yours using the latest AmberTools:
> > http://ambermd.org/AmberTools-get.html )
> >
> > scott
> >
> >
> > On Wed, Apr 11, 2012 at 10:19:05PM -0400, Trent E. Balius wrote:
> > > 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.
> > >
> > > -----Original Message-----
> > > From: Gaurav Chopra <gaurav at compbio.washington.edu>
> > > To: Trent E. Balius <tbalius at aol.com>
> > > Subject: Re: help request about making mol2 files for dock
> > >
> > > 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
> > > >
> > > > ========


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