AMBER Archive (2002)

Subject: Re: FEP - ligand to nothing (or water)??

From: David A. Case (case_at_scripps.edu)
Date: Tue Oct 29 2002 - 08:24:47 CST

On Tue, Oct 29, 2002, Aldo Jongejan wrote:
>
> DETERMINANT IS ZERO IN CENMAS ... STOP
>
> INPUT INCONSISTENT IN SUBR. CENMAS
>
> I suspect this has something to do with the fact I let
> the force constants go to zero? I don't perform any
> bond-shrinkage.
>

So do I...you probably do not want to set force constants to zero in the
perturbed state...you mainly need to remove their interactions with the
environment.

What you are trying to do *is* hard...be sure you feel comfortable with
simpler free energy changes first, and understand the concept of always
using cycles, etc.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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