[gmx-users] GROMOS Force Field

[Justin Lemkul]

On 6/24/15 3:46 PM, Isser, Ariel Y. wrote:
> Hi,
>
>
> I just started working with GROMACS (version 5.0) about a month ago, and I am trying to tweak the .itp file auto-generated by the PRODRG server for a small molecule.
>
>
> When I was comparing the PRODRG charges to those listed in the ffnonbonded.itp file in the gromos43a1 directory, I noticed that the masses and charges for most of the atoms are listed as 0.000.
>
>
> Is that a mistake on my end or am I perhaps looking in the wrong directory?
>

The charges in ffnonbonded.itp are not used for anything; use the .rtp file as a 
reference for appropriate charges.  Some charges are zero for aliphatic groups 
because that's the way the united-atom model works.

Masses aren't zero in the force field.  There's probably some magic going on 
where masses are taken from atomtypes.atp instead.  GROMOS force fields are 
always the oddballs in terms of the way the files are handled.

-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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