And ACPYPE does (besides several others improvements) Alan
On 9 October 2013 15:24, xiao <helitr...@126.com> wrote: > Hi Alan, > > Thank you very much! The problem is solved. The reason is that amb2gmx > cannot distinguish the proper and improper dihedrals. > > Best wishes > > Fugui > > > > > At 2013-10-09 21:58:29,Alan <alanwil...@gmail.com> wrote: > >Hi, try ACPYPE. > > > >Alan > > > > > >On 9 October 2013 14:07, xiao <helitr...@126.com> wrote: > > > >> Dear all, > >> > >> I am doing membrane protein simulation by using amber force field. The > >> lipid force field parameters are from the lipid11.dat from Amber. > Firstly, > >> i got the xx.prmtop and xx.prmcrd files, and then i used amb2gmx.pl to > >> convert the xx.prmtop and xx.prmcrd files into gromacs files xx.top and > >> xx.gro files. However, i found there is some problem with the xx.top > files. > >> For example, there are two dihedral parameters, and they should be > same, > >> but in the xx.top file (gromacs form) ,they are different. I have no > idea > >> where the problem is from. > >> Any information is appreciated! > >> > >> Fugui > >> -- > >> 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 > >> > > > > > > > >-- > >Alan Wilter SOUSA da SILVA, DSc > >Bioinformatician, UniProt > >European Bioinformatics Institute (EMBL-EBI) > >European Molecular Biology Laboratory > >Wellcome Trust Genome Campus > >Hinxton > >Cambridge CB10 1SD > >United Kingdom > >Tel: +44 (0)1223 494588 > >-- > >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 > -- > 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 > -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 (0)1223 494588 -- 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
