[gmx-users] NMA problem

Rashmi rashkush at gmail.com
Fri May 6 10:05:32 CEST 2011

Dear All,

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.

With Regards,

Rashmi Kumari
Research Scholar
School of Computational and Integrative Sciences
Jawaharlal Nehru University
New Delhi- 110067.
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