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

From: Carlos Simmerling <>
Date: Tue, 19 Jul 2016 11:23:06 -0400

this sounds like a Gaussian problem, not an Amber one. Also I'm not aware
of an Amber95 force field, so you might want to check to see what Gaussian
uses by the citation, not a number.

On Tue, Jul 19, 2016 at 10:50 AM, Ross Cheloha <>

> 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.
> Best,
> Ross
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Received on Tue Jul 19 2016 - 08:30:03 PDT
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