AMBER Archive (2004)

Subject: Re: AMBER: PMF correction factor

From: David A. Case (
Date: Tue May 04 2004 - 13:01:18 CDT

On Tue, May 04, 2004, Harvey, David Richard wrote:
> I was wondering if AMBER 8 can implement PMF correction calculations for a
> double annihilation FEP experiment involving a ligand with two aromatic
> rings. Previous attempts with AMBER 7 have resulted in errors due to
> constrained rings and a different program altogether was recommended.
> Annihilating the ligand will undoubtedly cause PMF errors for this
> experiment and it would be very helpful to know of any improvements in GIBBS
> or SANDER in AMBER 8 which may solve this problem.

The gibbs program has been retired, and we do not anticipate any further
developments. Hence, all features of FEP are unchanged. Reasons for this
decision are described at

I have had good luck in annihilating things as large as tryptophan side chains
using the thermodynamic integration facilities in sander; here PMF corrections
are not needed. I can reproduce the results of Shirts et al. (JCP 119:5740,
2003) to within 0.1 kcal/mol. Note that gibbs has no way to handle either
long-range electrostatic or long-range van der Waals interactions, and so can
only handle problems where you are sure that such contributions cancel on two
sides of a thermodynamic cycle.



================================================================== David A. Case | e-mail: Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to