[gmx-users] Regarding pdb file of a polymer

Justin A. Lemkul jalemkul at vt.edu
Tue Jun 19 21:45:11 CEST 2012

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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