[gmx-users] top2psf.pl

[Justin A. Lemkul]

Faezeh Kargar wrote:
> 
> Dear All,
> 
> I used top2psf.pl to visualize bonds in my coarse grained simulation 
> with MARTINI ff. it worked well. my system contained a box of 1 protein 
> and several hundreds of water molecules. then I repeated the box to make 
> a bigger system with command below:
> 
> genconf -nbox 2 2 2 -f 1box.gro -o 8box.gro
> 
> Now I have 8 proteins.  to visualize, I make just proteins .gro file and 
> repair .top file  but I can't visualize bonds in my new system. I think 
> my .top file has a problem. I examined several ways, but without any 
> results. Please help me.

The script is only designed to work on a single molecule.  If your system 
contains multiple proteins, you would need to supply what effectively amounts to 
a merged topology of all these proteins.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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