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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>>
>
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Mon Nov 24 2014 - 10:30:02 PST
