[gmx-users] generation of the pdb file

Shura Hayryan shura at phys.sinica.edu.tw
Sat Aug 25 03:09:21 CEST 2007


Thanks John,
I will use pymol or some other program. I was just expecting that GROMACS has its own tool for that. 
Thanks again.

                                       Shura

n Thu, 23 Aug 2007 21:25:36 -0400, Sheyore Omovie wrote
>  
> I have used pymol to generate pdb files for simple polypeptides.
> You might want to check to see if it will meet your needs.
> Rgds
> John
> 
> > From: shura at phys.sinica.edu.tw
> > To: gmx-users at gromacs.org
> > Date: Fri, 24 Aug 2007 07:48:27 +0800
> > Subject: [gmx-users] generation of the pdb file
> > 
> > 
> > Hi,
> > I am new in GROMACS and MD though have some experience of MM and Monte Carlo
> > simulations. I have looked through the users archive as carefully as I could
> > but couldn't find the answer to my (probably very simple) question: 
> > how to generate pdb file if your peptide is not in PDB databank? T.e. suppose
> > I know only the aminoacid sequence and want to do a folding simulation or
> > simulated annealing starting from some random conformation. Then how to
> > generate a pdf file for GROMACS? Thanks.
> > 
> > Shura
> > 
> > --
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