AMBER Archive (2008)

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

From: Zhao, Zhen (zhaozh) (zhaozh_at_ucmail.uc.edu)
Date: Mon Aug 25 2008 - 10:04:34 CDT

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.

Thanks

Zhen
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