AMBER: Problem with the prmtop file generated by sleap and leaprc.amoeba in Amber 10.

From: Zhao, Zhen (zhaozh) <"Zhao,>
Date: Mon, 25 Aug 2008 11:04:34 -0400

Hi, All

I set up the prmtop files using sleap and leaprc.amoeba (the amoeba force field) in Amber 10. When running md simulations, there is an error message regarding "a residue defined by a fast 3-point water has only 2 bonds". I finally figured it out that the prmtop file uses WAT for the residue name of water, which turns on the shake method somehow.

I fixed it by using the JFASTW=4 flag. But I think this is a bug in sleap of Amber 10. Hope it can be fixed soon.


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Received on Wed Aug 27 2008 - 06:07:28 PDT
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