how to refine a covalent-bond inhibior?

[Gerard 'CD' Kleywegt]

If you add a patch to link your compound to your protein,
this will introduce some extra parameters that I suspect
may not be in your current set of parameters.
E.g., if your link would look as follows:


                     C3...
       ND1---C1---C2/
                    \C4...

this would introduce:
- bond ND1-C1
- angle ND1-C1-C2
If, e.g., C1-C2 were a double bond, this would also
introduce a torsion ND1-C1-C2-C3 (or C4) with a target
of either 0 or 180 degrees.
In addition, an improper to keep ND1 and its three
neighbours in a plane would be needed.

Hope this helps,

--cd