[gmx-users] how can we modify *.rtp file?

Justin Lemkul jalemkul at vt.edu
Thu Jan 22 14:44:58 CET 2015

On 1/22/15 8:34 AM, marzieh dehghan wrote:
> Hi every body
> we would like to simulate a covalent modification on a protein by gromacs.
> Based on gromacs tutorial, modification is introduced as a new amino acids,
> so we changed *.rtp file. As a trick, we used parameters in output file
> (*.top) of topolbuild and prodrug server to modify the *.rtp file. We
> filled Atom, atom type, atom charge and charge group fields in the amino
> acids.rtp, but we don't know how to determine gb_xx and ga_aa, etc?

These are essentially just preprocessor directives that label which interaction 
should be used.  Look in ffbonded.itp and you will see how each parameter is 
mapped to each sequence of atom types.



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


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