On Tue, Apr 30, 2002, Ge Zhou wrote:
>
> I want to use the TIP4P parameters included AMBER 7. In
> dat/leap/parm/frcmod.tip4p file, I found the angle of HW-OW-EP is 120.0.
> But the angle is 52.26 in original reference(JCP 1983,79,926). I want to
> know whether it is a mistake and why the mass of EP is 3.00. Can anyone
> tell me?
The angle parameter has to be defined (to get LEaP to produce a prmtop
file), but then it is ignored. The sander code ignores all bonds, angles,
and torsions that have EP atoms. It builds the locations of the EP atoms
(at every step) based on the positions of the "real" atoms; later the forces
and torques on the EP's are projected back onto the "real" atoms, in order
to take the next MD step. This means that the mass of the EP atoms
is also ignored.
We should "clean up" these files, but I do not think there is any actual
error.
...good luck...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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Received on Mon Apr 29 2002 - 22:17:49 PDT
