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

From: David A Case <>
Date: Wed, 20 Jul 2016 17:40:58 -0400

On Wed, Jul 20, 2016, Ross Cheloha wrote:

> Upon further inspection the MM force
> field for Gaussian09 is actually the most current version of Amber (so
> Amber16 I think).

It would be helpful if you could indicate use what "further inspection"
you used, since the conclusion is wrong, and other users may be reaching
the same conclusion.

There is no default force field in Amber, so references to the "most current
version" of the Amber force field are not accurate.

> >> 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.

Amber uses standard PDB/IUPAC atom names, and there are no hydrogens in either
his or trp that are named "H4". I wonder if Gaussian is assigning these
names, or if there is some confusion between atom names and atom types (Amber
does have an atom type called "H4"), but having an MM hydrogen move away from
its bonded carbon is clearly a bug somewhere.

Amber supports QM/MM calculations with Gaussian, where Amber is "in charge"
and sets up the MM force field according to its conventions. If the nature
of the MM force field matters to you, this might be a better way to go.


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Received on Wed Jul 20 2016 - 15:00:02 PDT
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