Re: [AMBER] tleap neutralization bug?

From: Niel Henriksen <>
Date: Sun, 14 Sep 2014 13:29:41 -0700

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).


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 Sun Sep 14 2014 - 14:00:02 PDT
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