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

marzieh dehghan dehghanmarzieh at gmail.com
Thu Jan 22 14:34:10 CET 2015

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?

 thanks a lot


*Marzieh DehghanPhD Candidate of BiochemistryInstitute of biochemistry and
Biophysics (IBB)University of Tehran, Tehran- Iran.*

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