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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
>----------------------------------------------------------------------------
>---------
> Andrew D. Mesecar
> Assistant Professor
> Department of Medicinal Chemistry and Pharmacognosy
> and the Center for Pharmaceutical Biotechnology
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> Ear Mail 312-996-1877
> E-mail mesecar@uic.edu
> Just-da-fax 312-413-9303
> Spider-web http://www.uic.edu/labs/mesecar
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Dr. John J. Tanner
Department of Chemistry
University of Missouri - Columbia
125 Chemistry Building
Columbia, MO 65211
USA
office: 573-884-1280
lab: 573-884-1281
fax: 573-882-2754
tannerjj@missouri.edu
http://www.chem.missouri.edu/TannerGroup/tanner.html
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