I vote for figuring out what about ff12SB is breaking behavior that's been documented and working since at least Amber 8. Can that happen?
I have new parms and tests for glycam ready. The tests depend on what ff12SB does. I'd like to send in the tests now so they can be being tested. But, that one test will fail until ff12SB is in final form. Is that ok? Or, I can just test against 99SB if that is preferred.
PS: The reason Glycam has an "ROH" residue rather than an "OH" residue is because leap kept getting the residue name "OH" confused with, I think, the atom type "OH." I changed to ROH and, poof, it all worked.
:-) 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: B. Lachele Foley [lfoley.uga.edu]
Sent: Tuesday, March 20, 2012 9:32 AM
To: AMBER Developers Mailing List
Subject: Re: [AMBER-Developers] leap's impose behavior changed in past month
Yeah... sorry for the extraneous email. Was tired.
It's definitely something about "source leaprc.ff12SB" because if I "source leaprc.ff99SB", it works fine. And, if I hadn't been so tired, I would have tested that first.
:-) 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: Scott Brozell [sbrozell.rci.rutgers.edu]
Sent: Tuesday, March 20, 2012 4:15 AM
To: AMBER Developers Mailing List
Subject: Re: [AMBER-Developers] leap's impose behavior changed in past month
Danger, Will Robinson! Danger !
(aka, take a rest am-dev police, seriously off topic post,
yeah thats right, i just cluttered your inbox).
Klaxon
Lachele, Lachele u r 1 slick chick
and i aint talking 1.5 quick tricks:
leopard == tui
On Mon, Mar 19, 2012 at 11:41:29PM -0400, B. Lachele Foley wrote:
> PS: I sent this *before* reading today's xkcd. :-)
>
> Love coincidence. And leopards, particularly when they're clean, fast, and click at the right volume.
>
> Sent from my iPhone
>
> On Mar 19, 2012, at 9:19 PM, "B. Lachele Foley" <lfoley.uga.edu> wrote:
>
> > s/ N C CA O / N CA C O
Klaxoff
> >
> > ...or any reasonable variant. But, impose always was silent (on purpose, I think), if you asked for an angle it couldn't set.
> >
> > :-) 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: B. Lachele Foley [lfoley.uga.edu]
> > Sent: Monday, March 19, 2012 9:08 PM
> > To: amber-developers.ambermd.org
> > Subject: [AMBER-Developers] leap's impose behavior changed in past month
> >
> > The behavior of the impose command has changed since Feb 6. I don't pretend to be a biochemist, but I think the behavior as of the 6th was better.
> >
> > As of a git pull from Feb 6, the following worked:
> >
> > impose m3 { 1 2 3 4 5 } { { N CA C N 90.0 } }
> >
> > Now, it doesn't. I've tried a number of variants in terms of angle and atoms. I've tried backwards and forwards. Is this desired behavior? I can set equivalent-ish angles in carbohydrate builds.
> >
> > The current complaint is:
> >
> > impose: Illegal angle internal definition
> >
> > In better news, the leap tests I finally made are working fine.
> >
> > Sample leap input:
> >
> > source leaprc.ff12SB
> > m6 = sequence { NALA ALA ALA CALA }
> > impose m6 { 1 2 3 4 } { { N C CA O 120.0 } }
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Received on Tue Mar 20 2012 - 11:30:05 PDT
