[gmx-users] Potential issue using acpype to convert amber topology to gromacs

Easton J.W. jwe1g13 at soton.ac.uk
Wed Feb 14 23:28:49 CET 2018

Hi Justin,

Many thanks for the detailed reply.

I just wanted to check that it doesn't matter that the A2C and A3C are not present in the bonded and non-bonded itp files for the forcefield? Should this not have given an error?

Kind regards,

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: 14 February 2018 14:43:35
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Potential issue using acpype to convert amber topology to gromacs

On 2/14/18 9:42 AM, Justin Lemkul wrote:
> On 2/14/18 9:33 AM, Easton J.W. wrote:
>> Thanks Justin,
>> Will this effect the interactions (both bonded and non-bonded) that
>> these atoms have, as their atom types are not in the forcefield itp
>> files?
> Missing atom types would cause grompp to fail; you'd never get to the
> point where a simulation would be affected.
> You're introducing custom atom types in the topology itself, and
> that's always legal before any [moleculetype] appears. The LJ
> parameters come from the [atomtypes] directive. Masses and charges
> present in that directive aren't used.

Actually, to clarify: *if* masses are present in the [atoms] directive
of a [moleculetype], then the masses found in [atomtypes] are not used.
Strictly speaking, it is not necessary to have explicit masses in
[atoms], though nearly all topologies do.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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