On 2/14/18 5:28 PM, Easton J.W. wrote:
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?

The topology snippet you showed an [atomtypes] directive with those types defined, so they were in fact in the nonbonded parameter list by virtue of being added just above the first [moleculetype], as is permitted in GROMACS topologies. If there were missing parameters, grompp would have failed with a fatal error, so presumably you also included the necessary bonded parameters somewhere, too.

-Justin

Kind regards,

James
________________________________
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul 
<jalem...@vt.edu>
Sent: 14 February 2018 14:43:35
To: gmx-us...@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

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Virginia Tech Department of Biochemistry

303 Engel Hall
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Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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