Re: [AMBER] Questions concerning charges calculated by antechamber

From: Daniel Roe <>
Date: Mon, 28 Nov 2016 08:35:35 -0500


On Mon, Nov 28, 2016 at 7:36 AM, Andreas Gavrielides <> wrote:
> My first question is about the charges: The RESP and AM1/BCC charges I calculated are really different (differences can be of 0.60 e) for some atoms (C and N atoms). Is it OK?

It could be OK. The real question is, how well do the point charges
you obtain with either scheme reproduce the overall electrostatic
potential you get from QM? In my experience the two methods give
pretty similar results for most molecules, which makes sense since
AM1-BCC was designed to reproduce HF/6-31G*.

> Those given in gaff.dat file are all positive. I would like to know how they were computed.

Those aren't charges - those are atomic polarizabilities. Check here
for PARM file format info:

> My second question is about the bond, angle and dihedral parameters. Can I use them in the calculations independently the charges chosen? same parameters even if charges calculation scheme is different?

Well, sort of. In my experience you can usually use the same bond and
angle parameters, but torsions usually need to be refitted for new
charge schemes. The antechamber program tries to assign reasonable
parameters, but can occasionally miss (these are pointed out with
something like 'Needs attn' by the parmchk program).

Hope this helps,


Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Mon Nov 28 2016 - 06:00:16 PST
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