>Dear all,
>>Does someone how to get the best estimate for
>atomic charges in a NAD+ molecule?, as well as
>pK values of some of its protonable -OH groups.
>(or should I just take the pK from a ribose
>and a phosphate?).
>>I checked x-plor's topology.nad file and I found that
>the N atom (N1N) in the nicotinamide ring has a
>negative charge (-0.2). I always thought that
>this atom would be positively charged.
>>cheers,
>>Jordi
>>
Getting a good estimate for the charges on NAD+ appropriate for an MD
simulation without experimental restraints might take some work, but for
x-ray refinement the charges from topology.nad have worked fine for me.
Note that NAD+ has total charge=0 in topology.nad if you use hydrogens, and
-3.252 without hydrogens. If you are doing x-ray refinement you might as
well omit hydrogens and turn off electrostatics, as suggested in this news
group previously.
-------------------------------------------------------------------------------
Dr. John J. Tanner
University of Missouri - Columbia
Chemistry Dept.
123 Chemistry Bldg.
Columbia, MO 65211
phone: 573-884-1280
fax: 573-882-2754
chemjjt at showme.missouri.edu
-------------------------------------------------------------------------------
