Re: [AMBER] Bug or feature of tleap

From: Pengfei Li <>
Date: Tue, 2 Jun 2015 22:19:31 -0400

Hi Julio, Dave and Jason,

Thanks for the emails. I have changed the ff12SB to ff14SB force field,
deleted the "loadoff atomic_ions.lib" command in the tleap input file (to
prevent repeating) and added some comments about it in the webpage in
amber_web git tree. It may take several days for its showing up in the

Best regards,

2015-06-02 16:48 GMT-04:00 Julio Dominguez <>:

> Jason and dac,
> Thanks for you replies. I usually get the email digest so I take half a
> day before replying.
> >From what both of you mention now I understand that naming a
> user-generated library atomic_ions.lib (in my case, containing only zinc)
> will lead to trouble when tleap executes source leaprc.ff12SB.And yes, when
> I use my script the way it is, the atomic_ions.lib in the $AMBERHOME gets
> ignored and CL (or NA or K) are no longer seen when using the list
> command.That is what is happening. I guess I should NOT name my file
> atomic_ions.lib. I did not post the message because it was very
> uninformative:
> addIons: Argument #2 is type String must be of type: [unit]
> addIons unit ion1 #ion1 [ion2 #ion2] UNIT
> _unit_ UNIT _ion1_ NUMBER
> _#ion1_ UNIT _ion2_ NUMBER
> _#ion2_Adds counterions in a shell around _unit_ using a Coulombic
> potentialon a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must
> beopposite in charge to _unit_, and _ion2_ cannot be specified).
> Otherwise,the specified numbers of _ion1_ [_ion2_] are added [in
> alternating order].If solvent is present, it is ignored in the charge and
> steric calculations,and if an ion has a steric conflict with a solvent
> molecule, the ion ismoved to the center of said molecule, and the latter is
> deleted....
> It was until I read about similar proteins that I realized that my
> user-generated file was the source of the problem. But I did not know why
> is automatically loaded. Now it makes sense.
> Then, it is a feature, right?
> Maybe a warning should be added in the tutorial?
> Best regards
> _______________________________________________
> AMBER mailing list

Pengfei Li
Ph.D. Candidate
Merz Research Group
Department of Chemistry
Michigan State University
AMBER mailing list
Received on Tue Jun 02 2015 - 19:30:02 PDT
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