[gmx-users] NMA problem
rashkush at gmail.com
Fri May 6 10:05:32 CEST 2011
I am using MM/PBSA to calculate protein-ligand binding affinnity using
GROMACS. I got stuck at entropy calculation stage, which can be broadly done
by two mthods i.e. Normal Mode Analysis and Quasi-Harmonic method.
Can anyone let me know that how minimization using distance based dielectric
(r-dielectric) with a prefactor of 4 can be done for normal modes
calculation using GROMACS.
Thanks in advance for any valuable suggeations.
School of Computational and Integrative Sciences
Jawaharlal Nehru University
New Delhi- 110067.
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