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

[Justin A. Lemkul]

Faezeh Kargar wrote:
> Dear Justin
> 
> Thank you for your reply. this simulation contains a peptide and water 
> in a specified pH. Do you think this .pdb file is correct.
> 

I have no way to assess whether or not it is correct.  As I have already told 
you, it is a plausible input file.  Beyond that, I cannot say, nor can anyone 
else but you.

-Justin

> Thank you
> 
> Kargar
>  >
>  >
>  > 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
>  >>
>  >
>  > --
>  > ========================================
>  >
>  > 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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-- 
========================================

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

========================================