[AMBER] pmemd simulation

From: Sofia Vasilakaki <svasilak.chem.uoa.gr>
Date: Wed, 13 May 2020 09:01:28 +0300

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

Thank you,

AMBER mailing list
Received on Tue May 12 2020 - 23:30:02 PDT
Custom Search