Re: [AMBER-Developers] significant recent tleap changes

From: B. Lachele Foley <>
Date: Fri, 11 Nov 2011 20:34:26 +0000

"I noticed that the *current* practice for adding 1-4 scaling factors into the topology file is actually broken by the recent changes."

You're talking just about the 1-4 scaling factors assigned to impropers? Since, typically, none of those atoms is actually a "4" at all, does it make sense to assign numbers? Do they just get ignored anyway?

I just added "Make tleap tests" to my calendar. Will have some soon.

:-) Lachele

Dr. B. Lachele Foley
Complex Carbohydrate Research Center
The University of Georgia
Athens, GA USA

From: Jason Swails []
Sent: Friday, November 11, 2011 2:54 PM
To: AMBER Developers Mailing List
Subject: [AMBER-Developers] significant recent tleap changes

Hello everyone,

I'm a little concerned about tleap and all the changes it's been seeing
recently (not that it's creating bad topologies, yet). The recent changes
have caused a small test failure in the NAB directory due to the new IPOL
additions. However, this alerted me to what I considered a rather
deficient tleap test suite. The current tests
($AMBERHOME/AmberTools/test/leap) only test the creation of OFF library
files and old-style topology files(!) From the look of it, these are the
only tests we have for tleap, is this correct? (Except the indirect ones
like those in NAB).

I created a test in the leap directory (added to the default test suite) to
create an amber7 style topology (solvated and GB-ready) using an AmberTools
1.5 (fully patched) version of tleap. I noticed that the *current*
practice for adding 1-4 scaling factors into the topology file is actually
broken by the recent changes. The behavior we discussed in is no more (impropers no
longer get 0's, they get 1.2/2.0).

Do we want to go back to the original behavior (which would require adding
some of Arunima's original code back in) or just live with the new version?


P.S. -- Another note -- A topology file created prior to the 1-4 scaling
addition in tleap actually differed quite a bit from the topology file
created after the 1-4 scaling feature patch was added. It appeared under
slightly-more-than-just-skimming scrutiny to be a slight rearrangement of
some dihedral pointers, but I didn't do an exhaustive check. In any case
it'll be nice to be able to trace tleap changes through a more extensive
test suite (I don't think what I added was sufficient, but better than

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Fri Nov 11 2011 - 13:00:03 PST
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