How you converted the gaussian file into .pdb? Because once i did the same and suffered from some missing co ordinates.
Sent from my iPhone > On 08-Jul-2015, at 11:16 pm, Peter Stern <peter.st...@weizmann.ac.il> wrote: > > Look at the file: residuetypes.dat in the ../top/ directory of your > installation. > It lists all the residue names and more. > > Peter Stern > Weizmann Institute > > Sent from my iPad > >> On 8 ביולי 2015, at 17:45, Hamisu Aliyu Mohd <hamisu.kaza...@yahoo.com> >> wrote: >> >> >> Dear gmx-users, >> >> I am really new in this field of endeavour and I am trying investigate the >> solubility of peptides in organic solvents, I built a simple tripeptide >> (gly-gly-gly) using Gaussian 5.0 and I convert the output file(.out) to >> .pdb. I am now trying to use pdb2gmx tool to generate topology for my >> peptide using GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) I was >> promoted with an error "residue not found in residue topology database” I >> checked GROMACS website at http://www.gromacs.org/Documentation/Errors I >> learned the residue must have the same name as in the force field, please I >> don’t know the naming convention of this force field please HELP. >> >> Thanks >> Ali H. >> Department of Chemistry >> University Dutse >> >> -- >> 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. -- 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.
