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Re: [ccp4bb]: FMN and NAD - beware of atom type OS
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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
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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
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