[gmx-users] coarse grainig with Martini ff???

[Justin A. Lemkul]

Faezeh Kargar wrote:
> Dear All
> 
> I asked this question in Martini's forum, but tile now no answer, so I 
> had to ask it here. excuse me.
> I did an atomistic peptide simulation. The residues and positions of 
> all atoms in this peptide created by my self, I mean I didn't download 
> the pdb file from <www.pdb.org>. at the end of atomistic simulation I 
> have .pdb and .gro files that show the minimized structure of the peptide.
> 
> Now I have a question: Can I use the last pdb file for a CG peptide? Can 
> I use atom2cg.awk and seq2itp.pl in this case?
> 

You can run those scripts on any syntactically-correct .pdb file.

-Justin

> Thank you
> Kargar
> 

-- 
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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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