AMBER Archive (1999)

Subject: Re: Solvent - solute interactions

From: ross_at_cgl.ucsf.EDU
Date: Thu Apr 22 1999 - 13:45:26 CDT

The only energy analysis routine is ANAL; carnal has some
partly-written code that a serious programmer could consider
finishing. See the 'bugs' link on the amber web for ANAL
problems to watch out for.

You could get a reliable water-solute energy from sander by
breaking your system in 2, getting separate intra-water-water &
intra-solute energies, & subtracting from the total.

You'd have to manually fudge the box dimensions to be the same
as in the original, if there is a box.

Bill Ross