AMBER Archive (2006)

Subject: AMBER: klambda for TI method.

From: Biswa Ranjan Meher (brmeher_at_iitg.ernet.in)
Date: Tue Nov 07 2006 - 06:59:15 CST

Dear AMBER users,
For my protein-drug system: we are doing the free energy perturbations in a
transformation of ILE ---> VAL using the TI method. Now I am wondering which
klambda value should I use to get a better result. I tried to find this value
from the AMBER archive and found some questions and reply, but it didn't help
me clearly. Also for this I checked the section:5.6.18: "Free-energies using
thermodyanmic integration" in AMBER-7 manual where it is mentioned to refer Tom
Simmonson's article on Free-energy calculation
  (in Computational Biochemistry and Biophysics, edited by Becker, Mackerell,
Roux and Watanabe, New York: Marcel Dekker, 2001), but unfortunately this
article is not available here.

So I am not finding the source to know the right value of klambda for my
calculation. Can anybody please suggest which klambda value will be appropriate
for my calculation.

Thanks for your suggestions.

Regards
Biswa Ranjan Meher
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu