On 10/1/12 8:52 AM, venkatesh s wrote:
Respected Gromacs Users,
i am trying to simulate protein peptide
want understand interaction
my protien 210 Amino acid and my peptide only 5 Amino acid, and molecular
types different (between protein peptide )
docked conformation (may i follow Protein ligand tutorial )
No. You should process the peptide ligand with pdb2gmx, not any external
topology producing sites.
inserting peptide into pdb file
or
which suitable way i want do in gromacs ?
Either will work. The syntax of the coordinate file is all that matters.
pdb2gmx can handle multiple proteins in the same file, provided they are
separated by TER or have different chain identifiers. pdb2gmx should then
produce two topologies (.itp files), one for each protein (the larger protein
and the peptide ligand).
-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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