Re: free energy in sander

From: David A. Case <>
Date: Thu, 10 Apr 2003 15:45:05 -0700

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:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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Received on Thu Apr 10 2003 - 23:53:00 PDT
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