Re: [AMBER] bad atom type: Ng (*.prmtop files from tleap)

From: Jason Swails <>
Date: Thu, 07 May 2015 09:49:24 -0400

On Thu, 2015-05-07 at 09:04 -0300, Carlos Modenutti wrote:
> Hi,
> My system is a protein-carbohydrate complex solvated in TIP3P. The issue
> I'm having is related to how Tleap handles certain Atomic Numbers, and I
> first discovered it when attempting a 'GBSA &decomp' calculation using a
> solvated *.prmtop, it gave me the following error:
> bad atom type: Ng
> Ng is just the nitrogen of the amine group of a 3-substituted
> beta-N-Acetylglucosamine sugar moiety (Glycam resname is 3YB)
> When I checked the *.prmtop, I found that Tleap assigned the Ng Nitrogen
> atomic number as "-1" instead of "7"... However, upon stripping the
> *.prmtop, cpptraj somehow corrects this situation, replacing the "-1" with
> a 7.
> I'm a little confused, what does this "-1" mean in solvated *.prmtops?

It means that tleap didn't know what the element of that atom type was.
This information is usually given to tleap in the leaprc file (via the
"addAtomTypes" command). Look in
$AMBERHOME/dat/leap/cmd/leaprc.GLYCAM_06j-1 for where Ng is defined.
When you are using GLYCAM_06j, you should be sourcing that leaprc (not
just loading the parameter set) to make sure the other information is
properly added.

For the time being, I think atomic number information is just used when
assigning certain GB parameters, so if you're not using GB then it won't
really matter, I don't think.

> how
> does cpptraj recognizes and corrects it afterwards ?

I may be mistaken here, but I think cpptraj sees the "N" and figures
Nitrogen is the best match for the element.

> I'm using Glycam_06j and AMBER 14, by the way.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu May 07 2015 - 07:00:03 PDT
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