Re: [AMBER] Derive charge of multiple molecules

From: Jason Swails <>
Date: Thu, 19 Jun 2014 15:02:16 -0400

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,

[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
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Jun 19 2014 - 12:30:02 PDT
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