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Quoting AJANI HARESH <ajani_har...@yahoo.co.in>: > Respected Sir, > > > I am HARESH AJANI from CADILA HEALTHCARE LTD, INDIA. > > I am using gromacs at my Department of Bioinformatics. > > I am going to simulate an enzyme complex taking a ligand at active site and > another ligand at allosteric site. > > When I ran md simulation taking ligand at active site only then it was ok. > But when I am running the simulation taking both they show "moleculetype DRG > is redefined" > > > my topolgy look like this > > #include "ffG43a1.itp" > > #include "rrg.itp" > > #include "drg.itp" > > and at the end it is like this > > > > Protein 1 > > RRG 1 > > DRG 1 > SOL 10 > > SOL 17662 > > > > I can not understand why GROMACS takes into account bcause they are far apart > or is there any wrong to my pdb file. I am genereting the coordinate and > topology using PRODRG server. > The problem has nothing to do with your coordinate file. PRODRG, by default, names all of its [moleculetypes] "DRG," so you need to assign a proper name in this directive. Presumably, you want one of them to be RRG, but it is not set as such in rrg.itp. As always, beware the quality of PRODRG topologies: http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips -Justin > Please help me to find out the problem. > > --------------------- > HARESH AJANI > 09377756124 > ajani_har...@yahoo.co.in > > > ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 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 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