VMD-L Mailing List

From: Deepshikha Ghosh 19310001 (deepshikha.ghosh_at_iitgn.ac.in)
Date: Mon Dec 12 2022 - 04:23:41 CST

Dear VMDUsers,

I am trying to calculate the binding energy between two proteins using the
BFEE plugin of VMD. Even by specifying the protein (segname PP1) and ligand
(segname PP2 PP3) with their segment names respectively, BFEE is
considering the entire complex both as protein as well as ligand. Can
anyone suggest how I should define protein and ligand each, so that BFEE
considers them as two separate chains while generating the inputs for
calculation of PMF ?

Any kind of help will be much appreciated.

Thanks & Regards
Deepshikha