Hi Charles,
I'm using the newest Xplor-NIH 2.40. I meet problem when I tried to add
atom-based parameter for my ligand. I follow the manual, here is an example:
BOND ( name C3C and resname CYC ) ( name CAC and resname CYC ) 222.500
1.5292
when I tried to generate an extended structure, the software complained
parameters are missing for this bond. While it is all right when I applied
type-based parameter. I don't know what's wrong in my sentence.

The second question is, is there any way to put a rigid ligand into protein
cavity, and keep the ligand rigid during simulated annealing? The reason we
want to do this is, we already know the ligand conformation. But we don't
have enough NOE to reach such conformation in a random simulated annealing.
Thus we want to keep ligand rigid and let surrounding protein fit it--like
a reversed docking. Can Xplor-NIH do that?

Sincerely,
Qinhong Yu
Ames' lab
Department of Chemistry
UC Davis
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