回复: Re: 回复: Re: 回复: Re: 回复: Re: [gmx-users] about using amb2gmx.pl

Mark Abraham Mark.Abraham at anu.edu.au
Sun Feb 17 15:19:12 CET 2008

xi zhao wrote:
> Dear sir:
> Is my english weak?

Not particularly, but it isn't helping you describe clearly :-)

> I want to simulate pdb:1O5P (www.rcsb.org 
> <http://www.rcsb.org>), I use amber force field parms in the gromacs. 
> Under this condition, pdb2gmx can not produce chromophore top in the 
> pdb,

Why not? You need to tell us why it doesn't work!

> so I use antechamber and amb2gmx.pl to produce chromophore gro and 
> top files accoding to ffamber website. I do not know how to produce gro 
> and top of entire system.

Search the GROMACS wiki for "topology file" and read chapter 5 of the
GROMACS manual to work out how to turn your chromophore .top into an
.itp file suitable to include in a GROMACS .top file. Then use whatever
technique works for you to do the same with your structure file *without
the chromophore* (e.g. pdb2gmx, or via leap and amb2gmx.pl). Then
#include your chromophore .itp in that .top file, and give your
protein+chromophore structure file and that last .top file to grompp.

You will need a detailed knowledge of chapter 5 of the manual, and
there's useful information on the wiki too, so read them!


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