[gmx-users] problem with the amb2gmx.pl

Alan alanwilter at gmail.com
Wed Oct 9 15:58:29 CEST 2013

Hi, try ACPYPE.


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
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588

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