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

From: David A. Case <>
Date: Wed, 22 Dec 2004 13:50:00 -0800

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?


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Received on Wed Dec 22 2004 - 21:53:00 PST
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