Thank You Mr. Peter I just checked your response and that really helps. Gaussian allows you to save the file in different format(.pdb inclusive), I just choosed to save in .pdb format. I don’t know if I did the right thing. hahaha... On Jul 9, 2015, at 8:17 PM, su <sun.i...@gmail.com> wrote:
> Peter, This question was for Ali.H.. 😉 > > Sent from my iPhone > >> On 09-Jul-2015, at 5:20 pm, Peter Stern <peter.st...@weizmann.ac.il> wrote: >> >> I never did that. >> >> >> -----Original Message----- >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se >> [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of su >> Sent: Wednesday, July 08, 2015 11:26 PM >> To: gmx-us...@gromacs.org >> Subject: Re: [gmx-users] pdb2gmx error "residue not found in residue >> topology database" >> >> 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. >> -- >> 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.
