From: Revthi Sanker (revthi.sanker1990_at_gmail.com)
Date: Tue Oct 22 2013 - 02:04:49 CDT
Dear all,
I am trying to estimate the binding energy of a protein-ligand system that
I have simulated using NAMD with CHARMM forcefield. I have come come across
MMPBSA and MMPBSA-like analysis all of which are based on AMBER
forcefield. I have also tried converting the charmm format to amber format
using the program CHAMBER, but I am getting errors in that as well. Is
there any methodology that uses CHARMM forcefield in NAMD for Binding
energy calculation without having to run simulations for protein, ligand
and protein-ligand complex separately? Kindly provide your valuable
suggestions on the same.
I am aware that the question I am posting has been reviewed may a times in
the mailing list but I was unable to get a concrete answer or methodology
on how to actually go about it. Kindly help me in this as I am beginner to
MD simulations.
Thank you for your help in advance.
Revathi.S
M.S. Research Scholar
Indian Institute Of Technology, Madras
India
______________________________________________
International Conference on Bimolecular Simulations and Dynamics
*Official website:*
http://cmsrv.iitm.ac.in/icbsd2013/
_______________________________________________
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:48 CST