[gmx-users] Questions about the topology file format

[Sotirios Dionysios I. Papadatos]

If I am not mistaken, and there is a chance that I am the length and force constant are used with grompp in ffbonded.itp in the force field directory. 
After the question mark everything else is indeed not read so it is mostly used by the users for clarification. But I believe that in the part that you posted it is used in case you want to add some optional parameters you remove the mark.
Hopefully I am right, but please if it is not much do double check my comments. 

________________________________________
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: Wednesday, June 3, 2015 8:58 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Questions about the topology file format

On 6/3/15 1:55 PM, Ebert Maximilian wrote:
> Hi there,
>
> I have two quick questions about the topology file format which I couldn’t find in the documentary. The semi-colon is giving me some headache. Is it always a comment which is written after?
>
> First:
>
> [ atoms ]
> ;   nr  type  resi  res  atom  cgnr     charge      mass       ; qtot   bond_type
>       1 opls_135     1   IPA    C1    1    -0.111600     12.01100 ; qtot -0.112  CT
>
> is qtot and CT used for anything and is it interpreted since it is after the ;
>

Everything after ; is ignored.

> Second:
>
> [ bonds ]
> ;   ai     aj funct   r             k
>       1      2   1 ;    1.5350e-01    2.5363e+05 ;     C1 - C2         CT - CT
>
> are the values for r and k here used since they are after the ; and what is C1-C2 and CT-CT used for and why another ;?
>

Not used for anything.  Whatever software you used to produce the topology
annotated it for whatever reason that the programmer decided was useful and in
whatever manner he/she liked.

-Justin

--
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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