[gmx-users] problem with the amb2gmx.pl

[Alan]

And ACPYPE does (besides several others improvements)

Alan


On 9 October 2013 15:24, xiao <helitrope at 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 <alanwilter at gmail.com> wrote:
> >Hi, try ACPYPE.
> >
> >Alan
> >
> >
> >On 9 October 2013 14:07, xiao <helitrope at 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
> >> --
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> >>
> >
> >
> >
> >--
> >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
> >--
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-- 
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