AMBER Archive (2002)

Subject: PMF calculations

From: Sophia Kondratova (x357l_at_unb.ca)
Date: Thu Apr 25 2002 - 08:30:11 CDT

Hello,

I have a question concerning "PMF bond contribution method", which is used to
calculate the intra-perturbed group interaction contributions to the free
energy while doing FEP calculations (NCORC and INTPRT flag).

What other parameters besides NCORC=1 and INTPRT=1,2,3,4 or 5 have to changed
in order to calculate these intra-pert group contributions? I am trying to do
an FEP of guanine to adenine and when I set NCORC=1, I get values of ~600
kcal/mol, which is completely wrong (I do get the right answer with NCORC=0
and INTPRT=3)

Any help would be appreciated

Sophia Kondratova
Chemistry Department
University of New Brunswick
Canada