Re: [AMBER] Charged species with antechamber

From: Dr. Anselm Horn <>
Date: Thu, 10 Dec 2020 16:48:59 +0100


the tleap message you see is merely a warning, since you normally intend
to have systems with a total charge of zero (due to periodicity in the
simulation setup). So, no problem from that, you may add counter ions later.

Your other question "how good is antechamber at handling charged
molecules" actually relates to the "quality" of different charge
derivation methods, since antechamber acts just as front end for these.
Maybe you want to have a look into the literature (see citations in the
Amber manual) for a more in-depth discussion there.



On 12/10/2020 04:01 PM, Sam Walsworth (Researcher) wrote:
> Hi all
> I am aware that you can use antechamber to parameterise charged molecules (using the -nc flag) but I was considering if this is a reliable/tested method? I'm currently going through tLEaP and received an error saying 'The unperturbed charge of the unit (1.001001)<tel:+441001001> is not zero' which I'm assuming corresponds to my molecule having a -1 charge (-nc 1).
> My question is how good is antechamber at handling charged molecules? Are these error messages largely trivial or should I be cautious using this method (maybe would manually assigning charges from ab initio calculations be better?)
> Sam
> University of Huddersfield inspiring global professionals.
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Received on Thu Dec 10 2020 - 08:00:04 PST
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