Hi,
> if I understood well in Amber11 if one would like to calculate dG of
> decoupling
> of ligand from receptor using proper restraint it is enough to set
> parameter dvdl_norest = 1
> (to prevent including restraint contribution to dV/dl) and that.s all ?
that is enough to give you the dvdl without restraint contribution, which
I believe is what you want for this type of calculation. You still need to
actually set the restraint, e.g. using the nmropt functionality. The
restraint code was substantially changed since dvdl_norest was implemented
and I have no recent experience with it, so make sure you test the answers
you get on simple systems first!
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 06 2012 - 08:30:04 PST
