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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