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.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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Received on Thu Apr 10 2003 - 23:53:00 PDT
