AMBER Archive (2007)

Subject: Re: AMBER: Xleap and Hydrogens

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Nov 27 2007 - 11:11:35 CST


> > I was wondering if it was possible for XLEAP to add only
> > polar hydrogens or add no hydrogens at all.
>
> There is a united atom force field (ff03ua) that only includes polar
> hydrogens. But water molecules are usually the biggest contributor of
> hydrogens to a simulation system, and there is no way to remove those.

Back when leap was first being prepared for release, it was discovered
that the new method of applying improper torsions introduced by leap
did not work for the nonplanar cases seen in the united atom force field,
bacause the ordering of atoms around the central one could not be
guaranteed. Was this ever resolved?

Bill
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