On 9/28/12 10:07 AM, venkatesh s wrote:
Respected gromacs Users,
i want perform stimulation for
protein + peptide (in water medium only not membrane protein)
1. Can i use the Docked conformation (better conformation both protein +
peptide make it as one file .pdb ) for perform simulation
Yes.
2. Other than that manually edit the coordinate file after TER or END
insert peptide amino acid (my peptide having a 5 amino acid )
I don't understand what you want to do here. pdb2gmx can deal with multiple
proteins in a single coordinate file, with topologies written for each depending
on what you choose for the -chainsep option. Different chain identifiers or TER
delimiters can be used to indicate that a new molecule has started.
-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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