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[ccp4bb]: NAD and Osmium/Oxygen confusion

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While we're on the subject of NAD...

This is probably overkill since we don't use hydrogens or electrostatics
during refinement, but there is a proper NAD force field suitable for MD
simulations without experimental restraints.  I'm not sure how it performs
in X-ray refinement.

Pavelites, Gao, Bash, Mackerell, Jr. (1997)  A molecular mechanics force
field for NAD+, NADH, and the pyrophosphate groups of nucleotides.  J.
Comput. Chem. 18:  221-239.

In light of Andrew's comments about IUPAC naming, I should clarify what I
said about oxygen and osmium confusion in CNS.  The osmium confusion
involves atom "types" not atom "names".

>To all,
>    My experience with the NAD(P) and NAD(P)H structures available from the
>PDB as well as the downloadable topology and paramter files for CNS etc. is
>that they are not the best so I had to start from scratch.  First off, the
>available files do not allow for rotation of the carboxy-amide portion of
>the nicotinamide ring.  In a few 1.6 to 1.7 A structures that I have, you
>can clearly see a rotation.  I had to rebuild the molecules using small
>molecule x-ray coordinates and then I ran xplor2d to set-up the .top and
>.par files.  In order to do this, you have to make sure that any angles
>that you are interested in do not start out in a near planar geometry or
>the program will fix them as a plane for you.  I have these files available
>if any one wants them. They could even still use a little tweaking.
>     Also, if you use IUPAC naming schemes for the cofactors for atom
>names, it really helps avoid naming problems.
>   Andrew D. Mesecar
>   Assistant Professor
>   Department of Medicinal Chemistry and Pharmacognosy
>    and the Center for Pharmaceutical Biotechnology
>   (MC 870) MBRB Room 3070
>   900 South Ashland Avenue
>   Chicago, IL 60607
>   Ear Mail	312-996-1877
>   E-mail   	mesecar@uic.edu
>   Just-da-fax	312-413-9303
>   Spider-web   http://www.uic.edu/labs/mesecar

Dr. John J. Tanner
Department of Chemistry
University of Missouri - Columbia
125 Chemistry Building
Columbia, MO 65211

office: 573-884-1280
lab:    573-884-1281
fax:    573-882-2754