Thanks Lachele,
I missed out this trivial thing!
On 19 Apr 2016 16:59, "Lachele Foley" <lf.list.gmail.com> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
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>
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Received on Tue Apr 19 2016 - 00:30:03 PDT
