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 12:53:24 CET 2008

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 ?  

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

> 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.

It sounds like my earlier advice is appropriate. If you need to insert
your chromophore into your protein to form a complex to give yourself an
initial structure, then you will need to choose that protein structure
in a suitable conformation (this is not trivial) and then to "dock" that
chromophore. How easy it is to do the latter will depend on your
available experimental information. Google (or scientific literature)
searching for "docking" and "model building" is your best bet here -
it's well outside the scope of the GROMACS tool set.

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