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

xi zhao zhaoxiitc2002 at yahoo.com.cn
Sun Feb 17 13:34:53 CET 2008

Dear sir:
  Is my english weak? I want to simulate pdb:1O5P (www.rcsb.org), I use amber force field parms in the gromacs. Under this condition, pdb2gmx can not produce chromophore top in the pdb,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.

Mark Abraham <Mark.Abraham at anu.edu.au> 写道:
  xi zhao wrote:
> Easily, I have a pdb complex(pdb: 1O5P), I want to produce corresponding 
> gro top files, but I can only produce chromophore gro and top file using 
> amb2gmx.pl .Are you clear ? 

No. If you have a structure file already, then you need to read what I
wrote earlier. If you don't have a structure file already, then you need
to read what I wrote earlier. If you have some problem getting an
existing AMBER structure+prmtop to convert properly, then you haven't
communicated that. If you haven't got an AMBER structure+prmtop, then
give up on amb2gmx.pl

Try explaining your problem in English to a friend who doesn't fully
understand the science. Then apply the lessons you learned there to
describing the problem here :-)

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