Hi Everyone,
I have a question about Hvdw (as reported in Gohlke and Case, JCC, 2004,
25(2), p238). They used a 15A spherical solvent layer in computing this
parameter. What I want to know is the mechanics of doing this with
AMBER/ptraj. I am doing double trajectory MMGBSA and I have to do it by hand
(that is not using MMPBSA.py or pl). The VDWAALS energy in mdout files
contains both solute-solvent and solvent-solvent interactions. My question
is, do I do a single point on each solute+solvent snap shot, remove the
solute then do another single point and take the difference between these
numbers?
Thanks for your time!
Lekpa.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 16 2011 - 11:00:02 PDT
