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

From: Ross Cheloha <>
Date: Wed, 20 Jul 2016 10:53:04 -0400

Thank you for this reply, Carlos. Upon further inspection the MM force
field for Gaussian09 is actually the most current version of Amber (so
Amber16 I think).

I know this isn't a Gaussian mailing list, but does anyone have a tip
for tracking down the source of this strange behavior as it relates to
either Gaussian09 or Amber?

On 7/19/2016 11:23 AM, Carlos Simmerling wrote:
> 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 <>
> wrote:
>> 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 Wed Jul 20 2016 - 08:00:03 PDT
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