Dear Amber users,
I am running amber on a protein-ligand complex. The ligand binding site is
a rather flat, exposed surface, and thus in the production run, after about
10ns, the ligand moved away from the site. To avoid this, I am thinking to
add a small harmonic restraint (like 1 kal/mol?) to the ligand in the
production run.
Does anyone have experience with this kind of problem? It will be much
appreciated if anyone could give some suggestions.
Thanks,
Nadia
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Received on Wed Aug 27 2014 - 17:30:02 PDT
