AMBER Archive (2006)

Subject: Re: AMBER: klambda for TI method.

From: David A. Case (case_at_scripps.edu)
Date: Tue Nov 07 2006 - 10:06:21 CST

On Tue, Nov 07, 2006, Biswa Ranjan Meher wrote:
>
> For my protein-drug system: we are doing the free energy perturbations in a
> transformation of ILE ---> VAL using the TI method.

You should probably do this in two phases. First, remove the charges from ILE,
using klambda=1. Then, change the vdW parameters from ILE -> VAL, using
klambda >=4. Values between 4 and 6 have been used, but 4 itself should be
fine.

...good luck...dac

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