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
