Re: [AMBER-Developers] Amber atom type naming (and parms)

From: B. Lachele Foley <>
Date: Thu, 15 Dec 2011 20:55:32 +0000

There's also the issue of type HO which causes the catastrophic failure in those few circumstances where the right charged things all line up in just the right way. A tiny vdW term fixes it. Was mentioned last meeting.

  HO 0.2000 0.0300 M.B. Tessier 2011, use by permission only

I think you were considering adopting it. Still?

BTW, I'm thinking of making variants on leaprc.99SB-GLYCAM06 just to minimize confusion, but things like this will be important because if we put it in, it will get applied everywhere if our set is loaded last.

:-) Lachele

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

From: Piotr Cieplak []
Sent: Thursday, December 15, 2011 12:52 PM
To: AMBER Developers Mailing List
Subject: Re: [AMBER-Developers] Amber atom type naming (and parms)

Yes, we are going to test this new OS-P-OS in the context
of polarizable force field.


On Thu, 2011-12-15 at 06:46, David A Case wrote:
> On Wed, Dec 14, 2011, B. Lachele Foley wrote:
> >
> > * A conflict is introduced in parm10 -- the type CP (also long unused)
> > is being used again there. I just learned that today. I'm arguing that
> > we should give in on this one. Not sure if I'll win.
> Be sure to also check ff11: as Carlos indicated, there are also new atom types
> defined there.
> >
> > * We changed the params in angle OS-P-OS to a value that better fits
> > crystal structure data for nucleic acids, lipids and carbs. There is a
> > conflicting (and older) parm set in 94/99/10. Any chance y'all might
> > want to adopt ours?
> >
> > Older one: OS-P -OS 45.0 102.60 Parm94
> > Ours: OS-P -OS 45.0 109.6 Parm94 and changed eqm value for better
> > reproduction of average of crystal structures
> I should let Tom chime in here, but this sounds like a change that would need
> to be tested pretty broadly on DNA and RNA structures before being
> incorporated into our "recommended" nucleic acid force fields. One would want
> to be sure that a "better" local angle didn't indirectly degrade other
> desirable properties of the force field as a whole.
> ....dac
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