From: David A. Case <>
Date: Tue, 9 Sep 2003 08:32:58 -0700

On Tue, Sep 09, 2003, Ulf Johansson wrote:

> I'm trying to find out the Tip5p water model Amber paremeters. I'm looking
> in frcmod.tip5p. The bond parameters OW-EP for the extra points seems okay
> (the K-value is 553 and the distance is 0.7). The angle parameter is given
> as HW-OW-EP (the K-value is missing and the angle value is 109.47). This
> angle of 109.47, isn't this the angle between the extra points. If so
> EP-OW-EP should be specified I think? Also the torson parameters seem funny.
> There's no V/2 value. So both the angle and torsional parameters won't
> result in any force?

The way in which the "off-atom" points in TIP5P (and similar models)
are handled in sander is partially hardwired. You might want to look at the
code in extra_pts.f (search for "TIP5P"). Basically, the parameters you are
looking at in the frcmod.tip5p file are placeholders (which is why they have
zero force constants). The only thing that sander really needs to find there
are the OW-EP distance and the vdW parameters for OW.

> Finally Tip3p, Tip4p and Tip5p are basically rigid models I think. For
> example Tip5p is clearly ridgid in the Mahoney/Jorgensen article. But in
> Amber all those models seem to be flexible?

No, TIP3P, TIP4P and TIP5P are rigid in amber, since there are three SHAKEn
bonds, and the "off-atom" points are always constructed starting from the
positions of the three real atoms.

...hope this helps....dac

David A. Case                     |  e-mail:
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            |
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Received on Tue Sep 09 2003 - 16:53:01 PDT
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