[AMBER] About OH conformation in protonated Asp/Glu (ASH/GLH)

From: Marc van der Kamp <marcvanderkamp.gmail.com>
Date: Fri, 19 Jun 2015 12:29:02 +0100

Dear all,

I have noticed (in a few different projects/proteins) that when Asp or Glu
are treated as protonated (ASH/GLH), the hydrogen on OD2/OE2 can change to
a 'cis' position, i.e. the CB-CG-OD2-HD2 dihedral is ~0 degrees, as opposed
to the normal 'trans' position (with a CB-CG-OD2-HD2 dihedral of ~180
The .lib files of course define the hydrogen position to be in the normal
'trans' position, so the change to 'cis' happens during simulation.
This occurs with ff14SB for example (but also with the related force
fields, and quite possibly more), and usually when there is a good hydrogen
bond acceptor nearby. It then usually stays in this conformation for the
remainder of the simulation.

Have others noticed this?
Perhaps those that work with constant pH MD?

I am always somewhat suspicious when seeing such a cis conformation, as it
is not one I would expect to be very stable compared to the 'normal' trans
conformation (on QM grounds).
I must admit I haven't looked into this issue in any detail - perhaps
others have?
I would be grateful for any experience people have or know about (e.g.
references) regarding this issue.

Kind regards,
AMBER mailing list
Received on Fri Jun 19 2015 - 04:30:03 PDT
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