I got the reply ,
I will look in to Glycam documentation
thank you
On Thu, Aug 22, 2013 at 3:03 PM, Lachele Foley <lf.list.gmail.com> wrote:
> I will assume you found my earlier reply.
>
>
> On Thu, Aug 22, 2013 at 2:58 PM, lara lara <lara.4884.gmail.com> wrote:
> > Dear all
> >
> > Greetings !
> >
> > I am a new user of Glycam .
> >
> > I would like to build GAG molecule , for example
> >
> > the Alpha - iduronic acid 2 - O sulfate ( a single residue )
> >
> >
> > for that I called the xleap of amber ,
> >
> > 1) I sourced the ff99 force field.
> >
> > 2)I sourced the GLYCAM_06h-12SB
> >
> > 3)i loaded the Sulfate.prep
> >
> > then i did as given in the sulphating residue in Glycam
> >
> > m = sequence { ROH 0uA}
> >
> > set m.2.O2 charge -0.463
> >
> > set m tail m.2.O2
> >
> > m = sequence { m SUL}
> >
> > charge m
> >
> >>Total unperturbed charge: -2.000000
> >>Total perturbed charge: -2.000000
> >
> > I fixed the charge on the O2 atom as said , since the total charge should
> > be an integer.
> >
> >
> > when I tried to write the prm and top files
> >
> > it is giving the following error
> > Checking Unit.
> > WARNING: The unperturbed charge of the unit: -2.000000 is not zero.
> >
> > -- ignoring the warning.
> >
> > Building topology.
> > Building atom parameters.
> > Building bond parameters.
> > Could not find bond parameter for: Oh - S
> > Building angle parameters.
> > Could not find angle parameter: Cg - Oh - S
> > Could not find angle parameter: Oh - S - O2
> > Could not find angle parameter: Oh - S - O2
> > Could not find angle parameter: Oh - S - O2
> > Building proper torsion parameters.
> > ** No torsion terms for Cg-Cg-Oh-S
> > ** No torsion terms for Cg-Cg-Oh-S
> > ** No torsion terms for Cg-Oh-S-O2
> > ** No torsion terms for Cg-Oh-S-O2
> > ** No torsion terms for Cg-Oh-S-O2
> > ** No torsion terms for H1-Cg-Oh-S
> > Building improper torsion parameters.
> > old PREP-specified impropers:
> > total 1 improper torsion applied
> > 0 improper torsions in old prep form
> > Building H-Bond parameters.
> > Parameter file was not saved
> >
> >>>>>>>>>>>>>>>>>>>>>>>>>>
> >
> >
> > can any one let me know what is wrong and is the sulfation done here is
> > correct ?
> >
> >
> > Thank you
> > _______________________________________________
> > 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Aug 22 2013 - 12:30:03 PDT
