sangeeta kundu wrote:
Dear all,
I am trying to perform simulation of a protein with several ligands,
in case of certain ligands I found that the ligand is coming out of the
protein after 5-6 ns. I have checked the energy of the system, but it
does not show any abrupt change, still the ligand is coming out of
protein after a certain time.Is it due to steric hindrance during the
course of the simulation or something else? I can not debug, please
help. Thanks in advance.
Several possibilities:
1. You have lousy parameters for your ligand.
2. Periodicity effects (search the archive).
3. The ligand doesn't bind strongly, so this is normal.
#1 and #2 are the most likely, given the time scale you've used.
-Justin
regards
Sangeeta
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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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