Did you change your serine residue name to OLS? You need to make sure
that leap uses our special amino-acid residues for the linkage.
On Tue, Apr 19, 2016 at 1:17 AM, Neha Gandhi <n.gandhiau.gmail.com> wrote:
> Hi,
>
> I am trying to build O-glycosylated peptide (glycosylation at Serine).
>
> I first loaded ff14SB using tleap and then loaded Glycam06_j force field.
>
> I have linked the O-glycosylated residue 0YB to ser and saved the pdb file.
> When I am trying to check the pdb file to build amber topology, it gives
> following message below: I think it is mismatch in atomtypes (old
> nomenclature??).
>
> Could not find angle parameter: HO - OH - Cg
> Could not find angle parameter: OH - Cg - H2
> Could not find angle parameter: OH - Cg - Os
> Could not find angle parameter: OH - Cg - Cg
> Could not find angle parameter: 2C - OH - Cg
>
> How can I fix it?
>
> --
> Regards,
> Dr. Neha S. Gandhi
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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Tue Apr 19 2016 - 00:00:04 PDT
