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
residues).
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
--
========================================
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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