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<font size="2"><b>Thanks John,
<br />I will use pymol or some other program. I was just expecting that GROMACS has its own tool for that.
<br />Thanks again.
<br />
<br /> Shura
<br />
<br />
<br />
<br />
<br />
<br />n Thu, 23 Aug 2007 21:25:36 -0400, Sheyore Omovie wrote</b>
<br />>
<br />>
I have used pymol to generate pdb files for simple polypeptides.
<br />>
You might want to check to see if it will meet your needs.
<br />>
Rgds
<br />>
John
<br />>
<br />> > From: shura@phys.sinica.edu.tw
<br />> > To:
gmx-users@gromacs.org
<br />> > Date: Fri, 24 Aug 2007 07:48:27 +0800
<br />>
> Subject: [gmx-users] generation of the pdb file
<br />> >
<br />> >
<br />> > Hi,
<br />> > I am new in GROMACS and MD though have some
experience of MM and Monte Carlo
<br />> > simulations. I have looked through
the users archive as carefully as I could
<br />> > but couldn't find the
answer to my (probably very simple) question:
<br />> > how to generate pdb
file if your peptide is not in PDB databank? T.e. suppose
<br />> > I know
only the aminoacid sequence and want to do a folding simulation or
<br />> >
simulated annealing starting from some random conformation. Then how to
<br />>
> generate a pdf file for GROMACS? Thanks.
<br />> >
<br />> >
Shura
<br />> >
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