[AMBER] Proton wanders away from tryptophan and histadine sidechain carbon

From: Ross Cheloha <ross.cheloha.gmail.com>
Date: Tue, 19 Jul 2016 10:50:53 -0400

I am running a Gaussian 09 quantum mechanics/molecular mechanics
geometry optimizations using an Amber95 force field for the MM region. I
have seen that the protons (specifically H4 by Amber numbering) of some
histidines and tryptophans that are in the MM region move away from the
carbon to which they are bonded/associated for unknown reasons.

Has anyone seen this before or have an idea why I might be seeing this?
It seems to be a problem in the calculations/input files since it
doesn't make sense chemically. I can freeze these atoms to keep them
from moving but I do need to unfreeze everything eventually for the
final geometry.

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Received on Tue Jul 19 2016 - 08:00:02 PDT
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