[gmx-users] Re: Regarding pdb file of a polymer

sreeta.g sreetasai at gmail.com
Tue Jun 19 22:49:19 CEST 2012

Hi Justin
Thank you for the reply. However, PRODRG is used to generate topologies
from simple pdb files. I am clear on how to create the pdb files for
polymers in general (The entire long chain, with as many molecules as
required, using MS modelling.) My question, however is about how to arrive
at the pdb file. The pdb file that is described in the earlier procedure
has groups EthB, Eth, EthE and I am surprised because these groups are
neighboring groups in the pdb file mentioned, which is not intuitive. I am
interested in knowing how to create the pdb file using the beginning middle
and ending groups as described in the tutorial (rather than the entire
length of chain).
Thank you

On 19 June 2012 15:46, Justin A. Lemkul [via GROMACS] <
ml-node+s5086n4998712h3 at n6.nabble.com> wrote:

> 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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Sreeta Gorripaty

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