On 6/19/12 3:17 PM, sreeta.g wrote:
Hi
I am working with Polyvinyl Alcohol polymer. I have been following
http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html
(procedure by Justin) this thread for a lot of guidance. I have obtained the
coordinate file for PVA from other sources, however, I am unable to
understand how the coordinate file was written in this format. All other
sources of pdb files for polymers contain a fixed number of atoms and the
entire chain is written in the coordinate file.
Please direct me on this as to how the pdb file mentioned in the link has
been created.
I created it with a simple molecule drawing program, probably PRODRG but I
honestly don't remember. It's a toy example, meant to be extremely simple in
order to illustrate the necessary concepts. Creating a topology for propane is
otherwise very easy ;)
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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