[ccp4bb]: covalent linkage

["Martin K. Safo" <msafo@hsc.vcu.edu>]

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I am sorry this is not a CCP4 question, but I am sure somebody could
help me. I am using CNS to refine a a protein which has the N-terminal
Val amino group covalently linked to a ligand. I have patched this
ligand to the Val and also defined in the parameter and topology files
of the ligand the necessary bond distances and angles involving the new
bond.  This is a reduced schiff base and I expect bond distance of ~1.3
A. My delima is, as soon as I submit the model for minimization or
annealing the ligand moves away from 1.3 A to at least a distance of 2.2
A from the nitrogen of the Val. Please if someone could help me I will
surely appreciate it. Thanks.

Martin Safo