Re: [AMBER] Derive charge of multiple molecules

From: sunita gupta <>
Date: Sat, 21 Jun 2014 10:59:14 +0530

Thanks for the guidlines
Now in detail what I did with babel .mol2
I converted whole of the docked ligands into .mol2 using babel (.dlg ->
.pdb -> .mol2 ) babel by default uses Gastieger charge method.
Uisng this .mol2 I generated .prepin and .frcmod files using antechamber
and parmchk
At last when I used these files to make .prm and .crd files tleap gave me
following errors "
For atom: .R<LIG 1>.A<C1 1> Could not find vdW (or other) parameters for
For atom: .R<LIG 1>.A<C2 2> Could not find vdW (or other) parameters for
For atom: .R<LIG 1>.A<C3 3> Could not find vdW (or other) parameters for
For atom: .R<LIG 1>.A<C4 4> Could not find vdW (or other) parameters for
For atom: .R<LIG 1>.A<C5 5> Could not find vdW (or other) parameters for
type: ..... "

Below I am attaching the .mol2 file

Any help...

On Fri, Jun 20, 2014 at 12:32 AM, Jason Swails <>

> On Fri, 2014-06-20 at 00:08 +0530, sunita gupta wrote:
> > Hello Everyone,
> >
> > I want to do re-scoring of many docked complexes (pdb), for which I need
> to
> > make .prm and .crd files. As, it is not possible to process every ligand
> > individually, I need any method by which I can make prep and frcmod files
> > of all the ligands using antechamber with AM1-BCC charge method and
> without
> > specifying net chagre (-nc), as every ligand has different net charge.
> It seems you have a problem. If you want to use a QM method of any kind
> (semi-empirical, DFT, ab-initio, etc.), you need to know how many
> electrons you have. Ergo, you _cannot_ avoid inputting some net charge.
> You will need to find some way to determine net charge, even if it is
> determining the charge programmatically. Some programs in Amber are
> capable of chemical perception (like "reduce"), but I'm not aware of any
> that will determine net charge from an arbitrary PDB file. Of course,
> you also need all hydrogens to be present...
> > If, I am using .mol2 files, made using babel (Gastieger charge method),
> it
> > is giving error, and files are not made.
> This statement is mostly useless for anybody trying to help. We don't
> know what you tried [1] or what happened. Try to put yourself in our
> shoes and isolate the problem. We need enough information to reproduce
> or understand what went wrong but not so much information that we can't
> justify spending the time to wade through irrelevant details.
> Good luck,
> Jason
> [1] Paraphrasing or describing in words what you tried is not helpful.
> What people thought they did or tried to do is often different from what
> they _actually_ did -- only the exact commands, scripts, etc. that you
> used (along with the exact output) will tell us what you _actually_ did
> and let us help.
> When the description of the problem is vague, the root cause could be
> _anything_ -- user error or program bug. We (developers of any program,
> really) will assume the former until we can be reasonably convinced that
> the latter is true.
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list

Senior Research Fellow
Bioinformatics Centre
Jawaharlal Nehru University
New Delhi- 110067

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Received on Fri Jun 20 2014 - 23:00:02 PDT
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