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

From: Carlos Modenutti <cpmode.gmail.com>
Date: Thu, 7 May 2015 09:04:20 -0300


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? how
does cpptraj recognizes and corrects it afterwards ?

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

Thanks in advance for your support.

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Received on Thu May 07 2015 - 05:30:03 PDT
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