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