[gmx-users] Different charges in ffnonbonded.itp and aminoacids.rtp files.

[Justin Lemkul]

On 3/6/16 11:17 AM, Dawid das wrote:
> Dear Gromacs Experts,
>
> Why for some atomtypes the charges are different in ffnonbonded.itp and
> aminoacids.rtp files?
> For instance
> for         CD1     CA      0.035   8
> from TRP residue the charge for CA type residue is actually -0.115
> Does it mean that van der Waals parameters for this CD1 atom of Trp will be
> used as for
> the CA atom, but the charge will be 0.035 not -0.115?
>

The charges in ffnonbonded.itp are not used for anything.

-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

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