[gmx-users] interface_enrgy

shahid nayeem msnayeem at gmail.com
Mon Feb 7 14:18:14 CET 2011

Dear User
I am doing MD on protein complex keeping backbone as well as side
chain of all residues which is not on th interface fixed. For this I
prepared posre_backbone_sidechain.itp and defined this in .top file
for full MD. Now I want to know from the trajectory the best side
chain conformation of the interface residues for which I want to see
the change in total energy of the interface residues throught the
trajectory. I prepared index file for interface residues. But g_energy
command does not takes -n index.ndx to calculate energy of these
groups. How can I do that. Please suggest.
Thanking you

Shahid Nayeem

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