Dear AMBER users,
We are going to calculate the pka of a protonation of residue in a protein model, following the tutorial at
http://ambermd.org/tutorials/advanced/tutorial6/. I disabled the vdw interaction by setting the vdw radii of the hydrogen atom to 0.0 in the prmtop file (the term under %FLAG RADII). But it is strange that the vdw interaction didn't change w/o modification of the radii.
I am not sure whether I did it correctly or not and so request your suggestions.
Many thanks.
Jeffrey Yang
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Received on Sat May 08 2010 - 00:00:03 PDT
