Dear Amber User
I want to calculate " Average Interaction Energy " between residues in a
simulation box. For this I pack x molecules of A, y molecules of B and z
molecules of C in a box. After running MD for few ns now I have crd file.
Now from crd I want to calculate the average interaction energy between
residue A-A, B-B, C-C, A-B, A-C and B-C.
I read about MMPBSA from Amber Tools 12 manual and found that they discuss
about receptor and ligand only (only two system). While in my case the
system is different more than two and with in residue also.
Can any one please suggest me to how I will proceed to reach my goal. If
any other way to proceed this also welcome.
Thank you in advance
Regard
Rahman
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Received on Fri Apr 04 2014 - 02:00:02 PDT
