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Hello Martin--
>
> I have measured J couplings across hydrogen bonds, and they tell me
> that the hydrogen bonds must have a rather "nice" geometry, i.e. they
> must be short and straight. Is there a way to use this knowledge as a
> restraint? I have, of course, set distance restraints between the
> hydrogen bond donor and acceptor; how can I constrain the N--H-H angle
> to 180 degrees?
>
First, you might make use of the HBDB potential term and explicitly
specify the hydrogen bonds. This can be simply set up in the Python
interface by creating a restraint file file.tbl, and adding the code
snippet
protocol.initHBDB(restraintFile="file.tbl")
potList( XplorPot('HBDB') )
the format for file.tbl is to use statements like
assign ( acc and resid 99 and name O ) ( don and resid 103 and name HN )
for each hydrogen bond.
If you find that this term doesn't fix up h-bond geometry, please let me
know and we might try other approaches.
> I am using XPLOR-NIH version 2.16.0 on Mac OS 10.5.7.
>
you'll probably want to upgrade to a newer version.
best regards--
Charles
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