It helps a little, in that (I think) it confirms what I suspected. Some the carbohydrate FFs/parameter sets have a unique angle term for O-C-O (anomeric) and unique O atom type for the anomeric O. This corresponding 'modification' in nucleosides is what I was referring to.
Steve
Steven M. Graham. Ph.D.
Associate Professor
Department of Chemistry
St. John's University
8000 Utopia Parkway
Queens, NY 11439
718-990-5217
grahams.stjohns.edu
-----Original Message-----
From: David A Case [mailto:case.biomaps.rutgers.edu]
Sent: Thursday, April 14, 2011 7:58 AM
To: AMBER Mailing List
Subject: Re: [AMBER] nucleosides
On Wed, Apr 13, 2011, Steven M. Graham wrote:
>
> Has Amber ever been modified to account for the anomeric and/or gauche
> effects. There are plenty of modifications to handle carbohydrates,
> but I do not seem to be able to find the corresponding modifications
> for nucleosides. I mean, sure, Amber was parametrized using nucleoside
> data...
I'm not sure what you mean by "modified" here. So-called anomeric
interactions play an important part in determining the sugar pucker profiles,
and such interactions have been a part of the parameterization of force fields
from the very beginning. In a qualitative way, one could point to the
presence of two-fold torsion terms, but torsions, electrostatics and
Lennard-Jones terms interact in a complicated way in ribose and deoxyribose.
The complete potential reproduces (to some level of accuracy) profiles from
quantum chemistry calculations that in turn contain anomeric effects.
But there won't be anything like a "modification" that incorporates
(previously missing) anomeric and gauche effects.
...hope this helps...others know a lot more than I do about this....dac
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Received on Thu Apr 14 2011 - 05:30:04 PDT
