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vivek sharma wrote:
Hi justin,
Thanks for your reply...
Actually I tried docking with autodock, but I am not happy with the
results I am getting, they are not showing the expected energy value and
interaction as reported in literature.
Well, then the first thing to look for is orientation. If AutoDock did not
produce the right orientations for your ligands, *maybe* MD will. Visual
inspection would be the most immediate thing to do.
Any other forms of analysis would be dependent upon your system. Do your
ligands form H-bonds with the amino acids of your receptor (g_hbond)? Do
contacts within the protein change, and/or what contacts between the ligand and
protein result (g_mdmat)?
Other than that, read the descriptions of the analysis tools, maybe they will
inspire you :)
-Justin
So, I want to try docking using MDS(to study ligand binding by MD) as
well as scoring docked results using MDS (running MD on docked
configurations).
And I am having no clue for the same, any suggestion or guidance would
be of great help.
With Thanks,
Vivek
2008/10/1 Justin A. Lemkul <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
vivek sharma wrote:
Hi There,
I am trying to run MD simulation for screening my docking
result, but I am not aware of what are the parameters and
analysis we can do for docking by using MD simulation.
That depends entirely upon the scope of your question and what you
want to learn. Are you running MD on docked configurations, or are
you trying to study ligand binding by MD?
What is it that you are trying to investigate? This question will
largely motivate what type of analysis you do.
-Justin
If anybody have tried the similiar things using GROMACS, Please
help me in this regard.
With Thanks,
VIvek
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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