Impropers get zeros. That happens in sleap-generated tops, too. Is ok, so far as we've been able to tell. The code deals elegantly with zeros.
:-) Lachele
Dr. B. Lachele Foley
Complex Carbohydrate Research Center
The University of Georgia
Athens, GA USA
lfoley.uga.edu
http://glycam.ccrc.uga.edu
________________________________________
From: Jason Swails [jason.swails.gmail.com]
Sent: Friday, August 12, 2011 12:50 PM
To: AMBER Developers Mailing List
Subject: [AMBER-Developers] tleap 1-4 scaling concern
Hello everyone,
I have a slight concern regarding variable 1-4 scaling as it's implemented
in tleap. Looking at one of the topology files created by tleap, it appears
as though several dihedral 1-4 scaling parameters are just set to 0 in the
topology file. However, it also appears these may correspond to ignored
scaling factors (as with multi-term dihedrals and impropers, etc.), so they
don't really affect results (hopefully). Indeed in a small test case,
hard-coding all of the 1-4 scaling constants to be 1.2 and 2.0 appears to
leave the results unchanged wrt the old topology file.
They are inverted as soon as they're read in, though, so "0" may not be the
most industrious of choices here... Is there something I'm missing?
Thanks!
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Aug 12 2011 - 10:00:04 PDT
