[gmx-users] problem with the amb2gmx.pl

[xiao]

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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