On Sat, Oct 8, 2011 at 3:10 PM, ITHAYARAJA <ithayar...@gmail.com> wrote:
> only 59 particle variation found out of 230 ligand coordinates. > > On 8 October 2011 12:22, ITHAYARAJA <ithayar...@gmail.com> wrote: > >> Dear Sir, >> >> >> I am actually simulating my protein with its ligand so I incorporated all >> ligand (3) coordinates to my protein .gro file and placed its .itp file >> also. I used gromas96 43a1 force field. >> >> I found following error when i was doing grompp for energy minimization. I >> went through FAQ and checked all but i couldn't find what exactly it was. >> >> So, I attached that files to you. I need your help to solve this >> >> Program grompp, VERSION 4.5.1 >> Source code file: grompp.c, line: 377 >> >> Fatal error: >> number of coordinates in coordinate file (GR_b4ion.gro, 66074) >> does not match topology (GR.top, 66015) >> > I used to count the atom numbers in .gro file and manually modify the topology to make them match. > >> >> -- >> ** >> Ithayaraja M, >> Research Scholar, >> Department of Bionformatics, >> Bharathiar University, >> Coimbatore 641 046, >> Tamil Nadu >> India >> > > > > -- > ** > Ithayaraja M, > Research Scholar, > Department of Bionformatics, > Bharathiar University, > Coimbatore 641 046, > Tamil Nadu > India > > -- > 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 >
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