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

Tue Dec 28 11:36:42 CET 2010

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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.
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. TheÂ 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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