On 7/9/12 9:48 AM, Ramya LN wrote:
Dear all,
I have done protein-ligand dynamics.I got the final gro file.When
converted to PDB, i observed that my active site has ligand but two
chains of teh protein got separated. What might be the reason for
this?should i consider this as an error in my simulation???kindly help
me in this regard.
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
-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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