AMBER Archive (2002)

Subject: valine to alanine example

From: Sophia Kondratova (x357l_at_unb.ca)
Date: Tue Apr 30 2002 - 10:23:21 CDT

Hello

I am trying to do the valine to alanine FEP example in the tutorials on the
AMBER website. I get the same delta G as on the web, when using the input
files provided, but the simulations are short, and various contributions are
not calculated. What is the actual "true" result (kcal/mol) for this
simulation? (has this been calculated in the literature previously)

I was also wondering if anyone has done this perturbation with the "PMF bond
contribution" (ncorc=1 and intprt=5, shake=3).

Any help would be greatly appreciated

Sophia Kondratova
Chemistry Department
University of New Brunswick
Canada