How to correctly restrain hydrogen atoms bonded to heavy atoms in a rigid body

lksbath

Hi all,

I'm making a rigid body of my organic molecule (benzimidazole) and I have used restraints to restrain bond lengths/angles of the heavy atoms and hydrogen atoms. When I run my jedit file the heavy atoms stay in sensible positions but the hydrogen atoms wonder to strange positions. How can I restrain the hydrogen atom positions so that they stay fixed to the heavy atom, in a sensible position? I'm using single crystal data.

Also, is there a torsion angle restraint? I can only find examples of Distance_restrain and Angle_restrain. I think this might solve the problem.

Thanks

johnsoevans

The best way would be to include the H's as part of the rigid body? There are examples on this in the technical reference manual.

The other possibility is to ride the hydrogens on their C (http://topas.dur.ac.uk/topaswiki/doku.php?id=h_ride&s[]=ride). This won't work if you have large rotations of your rigid body.

lksbath

Hi John,

I am also looking into a rigid body method (z-matrix) to sort out the hydrogen atoms and the rest of the molecule (meeting problems with that, please see other post by me). Thanks for pointing me towards the relevant section in the Topas wiki for the hydrogen atoms, I had not found that one in my searches.

Lucy