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

[Justin Lemkul]

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-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
>
> --
> ==================================================
>
> 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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-- 
==================================================

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
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================