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

[xi zhao]

Dear sir :
  In fact, I have a complex structure(which contains protein and chromophore), though I have known the usual procedure dealing with ligand or drug in the gromacs, such as Prodrg server. Now I want to use Amber force field, and must deal with chromophore molecule in the complex using amb2gmx.pl, then have chromophore.gro and top file. But when the simulation runs, I need a complex entire  gro and top files in order to run, but I do not know how to use existing top and gro files to produce entire gro and top . Are you clear?
  Regards!   

Mark Abraham <Mark.Abraham at anu.edu.au> 写道：
  xi zhao wrote:
> 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! 

Your use of terminology is unclear - and you can't afford this sort of
lack of clarity in science. pdb, gro and top are all generic file
formats. Your first email implied that you did have a file with your
initial coordinates. The above implies the opposite. If you lack a file
containing your initial coordinates, then you may need to do some
serious leg-work to get one, e.g. search the Protein Data Bank.

I'd also suggest you follow Justin's advice, and do some tutorial
material. If nothing else they should teach you by example some better
ways of describing these things! :)

Mark
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