pawan gupta wrote:
hello
How can we calculate binding free energy and electrostatics
potential for ligand-protein complex?
Binding free energy may require the calculation of PMF or the use of
thermodynamic cycles (both somewhat complicated procedures). If you want the
nonbonded energies between the protein and ligand, simply use energygrps, but
these values will not correspond to binding free energy. You may also be able
to use g_lie, but you will still have to set the appropriate energygrps and have
some idea about the parameters to set of -Elj and -Eqq.
-Justin
which parameter is required in mdrun input file for that?
I tried online manual but did not get output.
It is appriciable if any body have idea
Thanks in advance
Regards
Pawan Gupta
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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