AMBER Archive (2009)

Subject: Re: [AMBER] DG improper torsion problem, two missing parameters

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Fri Oct 09 2009 - 12:25:30 CDT

> I checked 'DG.prep' file(from xleap by typing 'saveamberprep DG DG.prep'),
> and I could see there are 8 improper torsions assigned for Guanine.

Good strategy, but the impropers written when saving a prep file are
all the ones that are topologically possible, which is a different
set from the ones that the ff actually applies. The applied ones are
determined by matching the impropers in the parm.dat file to those
in the topology - only matching impropers are used.

Bill

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