On 5/10/13 12:35 AM, Arunima Shilpi wrote:
Hello sir
As in the tutorial for umbrella sampling command
make_ndx -f npt.gro
you have selected two different groups as Chain_A as 19 and Chain_B as 20
If we have protein-ligand interaction whether we should have single group
of protein-ligand complex or we should use two different groups for protein
and ligand.
A single group makes no sense. Consider what chains A and B are in the tutorial
- the pulled and reference groups, respectively. Apply the same logic in your
system.
-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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