Thank your for your help Lachele and Jason. It was apparently the residue
numbers and also the hydrogens of that Asn. It is fixed now.
Best Regards,
Maryam
On Tue, Nov 25, 2014 at 2:18 AM, Lachele Foley <lf.list.gmail.com> wrote:
> Hi, Maryam: Also check: did you change the ASN residue to NLN? did
> you delete the extra hydrogen from the ASN?
>
> I can also help you offline (I have the files).
>
>
> On Mon, Nov 24, 2014 at 11:20 AM, Jason Swails <jason.swails.gmail.com>
> wrote:
> > On Mon, Nov 24, 2014 at 3:11 AM, maryam azimzadehirani <
> > maryamai1988.gmail.com> wrote:
> >
> >> Dear Amber users,
> >> I am trying to attach a glycan chain to an Asn of a protein. I used the
> >> bond command in leap for the bond between Asn and glycan ans also for
> the
> >> inter glycan bonds. but I am getting this error for these bonds:
> >>
> >>
> >> *bond: Argument #1 is type String must be of type: [atom]usage: bond
> >> <atom1> <atom2> [order]*
> >>
> >> My bond commands are:
> >> bond gp0.715.O4 gp0.716.C1
> >> bond gp0.716.O4 gp0.717.C1
> >> bond gp0.717.O6 gp0.718.C1
> >> bond gp0.717.O3 gp0.719.C1
> >> bond gp0.719.O2 gp0.720.C1
> >> bond gp0.420.ND2 gp0.715.C1
> >>
> >> would you help me with this problem?
> >>
> >
> > Use the "desc" command in order to get a description of each unit. I
> > suspect what is happening, according to your error message, is that *one*
> > of the atoms you specified does not exist. That could be because you
> never
> > created the unit gp0. Or one of the residue numbers 420, 715, 716, 717,
> > 718, 719, or 720 does not exist. Note that these residue numbers are NOT
> > necessarily the numbers in the PDB file -- LEaP orders residues starting
> > from 1 and going sequentially, so you need to use those numbers.
> >
> > Beyond that, we need more information about what you actually did (i.e.,
> > the full script and possibly the PDB file) to be of any more help.
> > However, the "desc" command should be able to help you figure out what
> the
> > problem was.
> >
> > HTH,
> > Jason
> >
> > Regards,
> >> Maryam
> >> _______________________________________________
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> > _______________________________________________
> > 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 Mon Nov 24 2014 - 21:00:03 PST
