You're going to have to remove the HO4 yourself and alter the charge
yourself.
I really suggest asking this on the GLYCAM mailing list. You're more
likely to get attention there from folks who know lots of little details
about systems like this. They can let you know if there's anything special
about how to handle the system.
GLYCAM-L Mailling list: https://listserv.uga.edu/cgi-bin/wa?A0=GLYCAM-L
On Fri, Dec 8, 2017 at 12:34 PM, Tarsis Ferreira <tarsis.ferreira.gmail.com>
wrote:
> 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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>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Fri Dec 08 2017 - 15:30:01 PST
