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

Justin A. Lemkul jalemkul at vt.edu
Tue Jun 19 22:54:03 CEST 2012

On 6/19/12 4:49 PM, sreeta.g wrote:
> 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

Well, it can also provide a simple way to generate coordinate files.  It's a bit 
less convenient now that you need a license key, but in any case, there are 
plenty of ways to generate coordinate files.  PRODRG isn't really convenient, I 
just recall using it in that particular instance.

> 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

It's not a very good polymer, per se, it's just an example.  It is a boiled 
down, instructional demonstration with a system that is as simple as possible 
while still maintaining all necessary features (starting, middle, and ending 

> 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).

The names were modified using a simple text editor.  You can have any arbitrary 
number of internal monomer units, the only requirement in the proposed workflow 
is that the beginning and ending residues have some unique names.  You can have 
a million internal monomers with the same name (Eth or whatever) as long as the 
ends are different.



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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