Dear all,
I would like to ask how the pmemd describe the interaction between an
aromatic ring and an anion.
What I have in my X-ray structure is an aromatic ring in close proximity
to an -Cys-S-S (-1) anion. The anion is closer to one of the carbon atoms
which, based on QM calculations, has a positive partial charge. During
the simulation, the aromatic ring moves away from the anion and, in some
cases, the molecule goes off to the solvent, although in the initial
(X-ray) pose is very well packed in the active site.
Any suggestions why this happening and how I could keep the molecule in
place.
Thank you,
Sofia
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Received on Tue May 12 2020 - 23:30:02 PDT
