Greetings all,
I am trying to make a box around a protein and ligand in explicit solvent,
so that binding events can be captured as shown in this paper:
http://www.pnas.org/content/early/2011/05/31/1103547108
The paper uses flat bottomed harmonic restraints to make the box and
prevent the ligand from floating away from the protein. I read advanced
tutorial 4 on distance restraints, but don't think this is going to help
make the box.
I'm a bit overwhelmed by the restraint section in the manual and was hoping
someone knew a good method for creating the box that could be used with the
GPU code in amber 12?
Warm regards,
Ranji
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Received on Sun Nov 17 2013 - 12:00:03 PST
