回复： Re: [gmx-users] about using amb2gmx.pl
zhaoxiitc2002 at yahoo.com.cn
Sat Feb 16 14:04:56 CET 2008
Dear sir :
Can you tell me a detail of procedure, I have only chromophore molecular top,but I need entire top and gro for pdb + chromophore!
Mark Abraham <Mark.Abraham at anu.edu.au> 写道：
xi zhao wrote:
> Dear all users:
> I want to simulate a system ( protein + chromophore). I
> have had chromophore.gro and its top file using amb2gmx.pl,but I find I
> can not use them to translate PDB( protein + chromophore) file into gro
> and top files properly. So I need your advice about further procedure!
> Thank you very much
You don't need a .gro file. See
The grompp utility will happily make a .tpr from your .mdp, your .top
file, and your well-formed .pdb file whose atom, residue and molecule
names and ordering matches the .top file. This last constraint also
applies to a .gro file!
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