Re: [AMBER] how to generate paramaters for GlcNH3

From: Tarsis Ferreira <>
Date: Fri, 8 Dec 2017 11:34:17 -0600


I’m sorry. After some digging I found that has the parameters for the protonated GlcNH3.

While trying to build a hexasaccharide using leap...

 source leaprc.GLYCAM_06j-1
 loadamberprep GlcNH2_and_GlcNH3.prep
 loadamberparams glcnh3.frcmod
 glycan = sequence { ROH 4ZB 0YNP }
 set glycan tail glycan.3.O4
 glycan = sequence {glycan 4ZB 0YNP }
 saveAmberParm glycan glycam.prmtop glycam.crd
 savepdb glycan glycam.pdb

for some reason it’s not deleting HO4, and I’m this error:

> glycan = sequence { ROH 4ZB 0YNP }
> set glycan tail glycan.3.O4
> glycan = sequence {glycan 4ZB 0YNP }
> saveAmberParm glycan disa.prmtop disa.crd
Checking Unit.
ERROR: The unperturbed charge of the unit: 0.194000 is not integral.
WARNING: The unperturbed charge of the unit: 0.194000 is not zero.

 -- ignoring the error and warning.

Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Could not find angle parameter: Cg - Oh - Cg
Building proper torsion parameters.
 ** No torsion terms for Cg-Cg-Oh-Cg
 ** No torsion terms for Cg-Oh-Cg-H2
 ** No torsion terms for Cg-Oh-Cg-Os
 ** No torsion terms for Cg-Oh-Cg-Cg
 ** No torsion terms for H1-Cg-Oh-Cg
 ** No torsion terms for Cg-Cg-Oh-Cg
Building improper torsion parameters.
old PREP-specified impropers:
 total 2 improper torsions applied
 0 improper torsions in old prep form
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Parameter file was not saved.
> savepdb glycan disa.pdb
Writing pdb file: disa.pdb
 Truncating residue name for PDB format: 0YNP -> 0YN
 Truncating residue name for PDB format: 0YNP -> 0YN

Can you tell me what have I done wrong?



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Received on Fri Dec 08 2017 - 10:00:03 PST
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