[gmx-users] generation of the pdb file

[Shura Hayryan]

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)
> > 
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
-----------------------------------------------------------------------
Find a local pizza place, movie theater, and [WINDOWS-1252?]more
.then map the best route! Find it!

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

 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20070825/73c73171/attachment.html>