AMBER Archive (2004)

Subject: Re: AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules

From: Jianwen Jiang (jiangj_at_che.udel.edu)
Date: Wed Dec 22 2004 - 15:59:47 CST

Yes, I am using Amber8, and the residue name of my crystal water is HOH.

I just checked the force field files, they are:

In leaprc.ff03:
----------------
HOH = WAT
TIP3 = WAT
TP3 = WAT

In leaprc.ff99 or leaprc.ff02:
----------------
HOH = TP3
WAT = TP3

I am not sure how the file handles the "HOH" and "WAT" residues?

"David A. Case" wrote:

> On Wed, Dec 22, 2004, Jianwen Jiang wrote:
> >
> > Previously, I used leaprc.ff03 force field ("source leaprc.ff03"), and
> > tleap failed. Instead, now I use "source leaprc.ff99", then tleap works.
> > All H atoms are added to the crystal water molecules in the same direction.
>
> This is weird: the handling of water molecules should be the same in
> leapr.ff03 and in leaprc.fff99.
>
> Are you using Amber 8? Could you look at these two files and see how they
> handle the "HOH" and "WAT" residues?
>
> ...thx...dac
>
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--
Kind regards,

Jianwen

-------------------------------------
Jianwen Jiang
Department of Chemical Engineering
University of Delaware
Newark, DE 19716
-------------------------------------
Tel: (302) 831-6953
Fax: (302) 831-1048

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