TANNER at BRAGG1.BCHS.UH.EDU
Fri Sep 20 18:42:32 EST 1996
>> I have seen that ignoring hydrogens leads to higher R-factors
>> and energy terms, particularly when solvent is used during the
>> refinement. Not sure how much this weighs against computational
>> But turning off charges on Asp etc has always been useful during
>> simulated annealing.
Are you deleting hydrogens but keeping electrostatics? That
causes a problem because hydrogens carry partial positive
charges to make the overall charge of most residues balance out
to zero. In the absence of hydrogens a protein with about
700 residues will carry a total charge of about -300!
So I would say either keep both hydrogens and electrostatics or
throw them both out.
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