Dear Charles,
Recently I have tested the water refinement script (Xplor-NIH 2.31).
The run completed fine, but upon inspection I noticed the aromatic
side chains had their planarity distorted. For example, CG-CD-CE-CZ
dihedral in Phe side chain was 4.8 degrees, the ring adopting a chair
conformation.
For topology/parameters initialization I have used the values in the
GB1 example:
protocol.parameters['protein']="waterRef/parallhdg5.3.pro.new"
protocol.parameters['water'] ="waterRef/parallhdg5.3.sol"
protocol.topology['protein'] ="waterRef/topallhdg5.3.pro.new"
protocol.topology['water'] ="waterRef/topallhdg5.3.sol"
protocol.initParams(("protein","ion.par"))
I was also surprised to see very little change in the side chains
after the run. Even in the scenarios where a positive and negative
residues were one turn from each other on an alpha-helix, there was
little side chain rearrangement.
Thank you,
Vitaly
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