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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>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Nov 24 2014 - 08:30:04 PST
