Dear Sangeun, Did you try ‘pdb2gmx’ using your structure file?
I checked NME and NHE are in the AMBER99sb-ildn forecefield. So, if pdb2gmx doesn’t work, you can draw NME and NHE using molecular viewer and then change residue/atom name to NME and NHE. Yoochan > On Apr 4, 2015, at 7:01 AM, sang eun jee <sangeun...@gmail.com> wrote: > > Dear gromacs users > > Hello. I have question how to decide terminal residue forcefield and put > them in library? > > I am using AMBER99sb-ildn forcefield in gromacs. Not like gromos or opls > forcefield, amber forcefield treat termini in its own way and current > version only works with NH3+ and COO-. I would like to termini as a neutral > status, NH2 and COOH and would like to modify forcefield to include this > specific termini data. > > To decide charges and parameters to describe specific termini, is there any > way to decide parameters based on non-terminal residue database? When I > looked at NGLY and GLY from animoacids.rtp, I could not find out specific > rules. > > Thank you very much. > > Sangeun Jee > -- > Post Doctoral Researcher > School of Materials Science and Engineering > Georgia Institute of Technology > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
