[AMBER] Problem re. non-integer charge in glycoprotein

From: RAJAS MALLENAHALLI RAO <rajas.mallenahalli-rao.univ-reims.fr>
Date: Fri, 14 May 2021 18:24:07 +0200

Hello all,

I'm using Amber to simulate a glycoprotein containing keratan sulfate
glycans with sialic acid cap. I built the system using glycoprotein
builder of glycam.org, and I replaced the glycosylated Asparagine
residues with NLN. I'm using ff14SB for protein & Glycam06-j1 for
sugars. When I loaded the protein on tleap and checked for its charge,
it gives me a non-integer value:

> test = loadpdb prot1a.pdb
Loading PDB file: ./prot1a.pdb
   total atoms in file: 4343
   Leap added 3978 missing atoms according to residue templates:
        3978 H / lone pairs
> charge test
Total unperturbed charge: -49.992000
Total perturbed charge: -49.992000

I tried to check where this is coming from, I tried on unglycosylated
system, it gives integer value; on glycosylated system (w/o any charged
residues as well as with sialic acid) it gives integer value. The
problem starts when I add the sulfate groups. Is it advisable to fiddle
with the NLN residue library to even out the non-integer value? or is it
safe to ignore it altogether? Many thanks for suggestions/ help in

Rajas M Rao
Postdoctoral researcher
Laboratoire MEDyC CNRS UMR-7369
Université de Reims Champagne-Ardenne
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Received on Fri May 14 2021 - 09:30:03 PDT
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