hydrogen bonds

Angelo Gargaro angelo
Fri Mar 8 03:30:09 EST 1996


Dear Xplor users,
		While doing a NMR structure calculation I have noticed that
my hydrogen bond distances (1.8-2.5 restraint distance) tend towards the upper
limit. A quick examination of the parrallhdg.pro file and the manual p50 shows
that for proteins there is only one van der Waals radius specified for
hydrogens
and that this effectively forces the lower limit of hygrogen-oxygen distances
to 
be approx 2.25 using repel=0.8. Has anybody else seen this effect and if so
have they modified the parallhdg.pro file in any way to overcome it. I was
considering just introducing a shorter vdW radius based on the value in the
CHARMM parameter set.

Angelo Gargaro
Division of Molecular Structure
National Institute for Medical Research
Mill Hill
London




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