[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
> >
> > --
> > Open WebMail Project (http://www.phys.sinica.edu.tw)
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