Hi,
I’m sorry. After some digging I found that glycam.org 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?
Thanks,
Tarsis
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Received on Fri Dec 08 2017 - 10:00:03 PST
