deleting hydrogens

[Jack Tanner]

Raman wrote:

>>
>> 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
>> efficiency. 
>>
>> But turning off charges on Asp etc has always been useful during 
>> simulated annealing.
>>
>> Regards
>>
>> Raman

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.

Jack Tanner