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

From: David A Case <>
Date: Thu, 15 Dec 2011 09:46:53 -0500

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.


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Received on Thu Dec 15 2011 - 07:00:04 PST
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