AMBER Archive (2003)

Subject: Re: free energy in sander

From: Joseph Fernandez (joefern9999_at_yahoo.com)
Date: Thu Apr 10 2003 - 21:58:30 CDT

you say in manual that if dummy atom is introduced in
peturbed state then integrand diverges and klambda
must be greater than zero. Does NH4+ (perturbed) to
NH3 (real) calculation present any problem using TI in
sander with klambda = 1?

--- "David A. Case" <case_at_scripps.edu> wrote:
> On Thu, Apr 10, 2003, Joseph Fernandez wrote:
>
> > AMBER 7 manual mention that Sander could be used
> for
> > free energy calculations (using TI) for OH -> O-
> > process (since vdW parameter for H bonded to OH is
> > zero). Could this be used for NH4+ to NH3 if
> dummy
> > atom is defined with zero vdW? If so does klambda
> > have to be greater than 1?
> >
>
> I guess it would depend upon how you defined the
> atom types of NH4+ and NH3.
> Note that in the amber ff94 force field, hydrogens
> bound to N (as in LYS)
> do *not* have a zero van der Waals radius. If you
> followed this, you would
> need to change both the charge and the radius to
> make one of the H-atoms a
> dummy atom.
>
> (I'm also not sure what thermodynamic cycle you are
> planning to look at...)
>
> ..hope this helps...dac
>
> --
>
>
==================================================================
> David A. Case | e-mail:
> case_at_scripps.edu
> 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 |
> http://www.scripps.edu/case
>
==================================================================
>

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