Re: [AMBER] tleap neutralization bug?

From: Marcus Arieno <>
Date: Mon, 15 Sep 2014 11:45:06 -0400

Out of curiosity, what type of simulation artifacts would one expect if the periodic system carries a net charge? I suspect such an issue might give slight density problems if running NVT simulations for a long time, but NPT should be more or less fine.

Any comments on this or relevant papers on the subject?

Marcus Arieno

On Sep 14, 2014, at 4:29 PM, Niel Henriksen <> wrote:

> Hi Alican,
> I've noticed this nuisance as well. I think it just a quirk of LEaP ...
> you aren't doing anything wrong. The best advice I have is to make sure
> all your ligands have integer charges before you start building the systems
> with leap. You could manually alter a few partial charges to get
> everything evened out. My solution was to make my automated scripts
> recognize this situation and add another ion when necessary.
> I thought (?) antechamber's behavior improved in Amber14 to only produce
> integer charges, but I could be wrong (or you could be assigning partial
> charges some other way).
> --Niel
> On Sun, Sep 14, 2014 at 11:28 AM, Gulsevin,Alican <> wrote:
>> Hello,
>> I couldn't find a similar topic in the archives list, so I wanted to
>> bring up the question. When neutralizing a protein (or protein-ligand
>> complex) using tleap, tleap has a weird propensity. If the charges
>> calculated for the ligand by antechamber make the system have a charge
>> like -15.001, tleap neutralizes the molecule with 15Na+ ions, realizing
>> that the charge is actually fifteen. However, when the system has a
>> charge of -14.999, instead of 15, tleap decides to titrate the molecule
>> with 14Na+, although it can recognize the system has a final charge of
>> -0.999. It causes particular hardship when I automatize my calculations
>> with a bash script, because I have to go back and change the charges
>> manually, use tleap again, etc. This was a problem I encountered with
>> Amber12, now I see the same thing happening with Amber14. I thought
>> someone should have mentioned it until now, not seeing any remark also
>> makes me think if I've been doing something wrong.
>> Any comments on this?
>> Thanks,
>> Alican
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Received on Mon Sep 15 2014 - 09:00:02 PDT
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