Hi all,
I have a problem with a simulation i'm running. I have a pdb file, which I have stripped and contains only protein, ligand, divalent metal and 4 cryst. waters (I removed the CONECT records etc). When I run a standard restrained minimization (similar to the restrained minimization protocol in Ross's tutorials) the 4 cryst. water appear distorted and only have a HOH angle of ~18degrees. Upon running a 2nd minimization, unrestrained the problem still persists and again the same, after a solvated cmd1 heating. The stripped pdb file looks fine, however, so I'm not sure what's going on. Has this been previously encountered? Could it be an imaging problem or is there some deeper problem?
Thanx,
Maura
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Received on Tue Aug 02 2011 - 15:00:03 PDT
