From: Ulf Johansson <>
Date: Wed, 10 Sep 2003 09:37:36 +0200

Thanks for yor reply,

I'm planning to simulate macromolecules in water and want to understand in detail how Amber treats the Tip3/4/5p models.

I've downloaded the parameter files and from them I first got the impression that the Amber Tip3p model is flexible (because K values are given for both the OW-HW bond and HW-OW-HW angle). Now, did I get you right in that this "flexibility" is then restrained by the Amber program, using a procedure called SHAKE, to render the Tip3p model inflexible (in the sense that the relative distances and angles between atoms never change), and that this also extends to the Tip4/5p models?

Also do you know why this restraining is done. Doesn't it remove the internal vibration energy modes from the Tip3/4/5p water models?

I yet don't have access to the Amber source code. Do you know of some other place, article or so, where I can find the parameters for the "flexible" description of the Tip4/5p models?


----- Original Message -----
From: "David A. Case" <>
To: <>
Sent: Tuesday, September 09, 2003 5:32 PM
Subject: Re: AMBER: TIP5P

> 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 Wed Sep 10 2003 - 08:53:00 PDT
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