Sorry, I didn't know about PRODRG. The use of it may be incorrect here, since the error highlighted concerns pdb2gmx.
2013/4/22 Justin Lemkul <jalem...@vt.edu> > > > On 4/22/13 5:30 AM, Baptiste Demoulin wrote: > >> Hi, >> >> You have to add an entry for the DRG residue in "aminoacids.rtp", in the >> gromos folder. Instructions on this can be found in the GROMACS manual >> http://www.gromacs.org/**Documentation/How-tos/Adding_** >> a_Residue_to_a_Force_Field<http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field> >> >> > This is not correct. PRODRG produces a topology (albeit a very flawed > one), so there is no need whatsoever to modify .rtp files since pdb2gmx > should never be involved in this workflow. > > -Justin > > > 2013/4/22 zyduscadila <haresh.aj...@zyduscadila.com> >> >> Dear Justin thanks for your email. >>> >>> I have tried those you mentioned in your email. >>> >>> I have submitted molecule of interest in PRODRG and got a DRG.itp or >>> DRG.pdb >>> file. >>> >>> I fired command pdb2gmx using DRG.pdb (obtained from PRODRG) using >>> Gromos96 >>> 43a1 force field , but I received the follwoing fatel error: >>> >>> "Residue "DRG" not found in residue topology database". >>> >>> Let me know, how to handle this error ? please give me a brief step how >>> to >>> do this ? >>> >>> I hope you will give me a solution. Thanks in advance >>> >>> Thanks & Regards, >>> >>> HARESH AJANI >>> >>> >>> >>> >>> -- >>> View this message in context: >>> http://gromacs.5086.x6.nabble.**com/Only-Ligand-Without-** >>> Receptor-MD-Simulation-with-**solvent-other-than-water-** >>> tp5007488p5007537.html<http://gromacs.5086.x6.nabble.com/Only-Ligand-Without-Receptor-MD-Simulation-with-solvent-other-than-water-tp5007488p5007537.html> >>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com. >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> * Please search the archive at >>> http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >>> posting! >>> * Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org. >>> * Can't post? Read >>> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> >>> > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
