[AMBER] glyco

From: yanyuna <hiyanyuna.gmail.com>
Date: Mon, 15 Oct 2012 16:59:46 +0800

Thank you very much.The following is what I have once asked and you have

" Most glycoproteins take a while to build and minimize, especially on
the current site. But, if it's really taking a long time, there might
be a problem with the builder. It doesn't work well with all pdb

I'm sure there are other ways to build the coordinates using other
software, but I don't know them.

Here are two things to try. Try either, both or neither, as it suits you.

1. Write me off-list or atglycam.gmail.com with your pdb file. I
can see if our site is having trouble with the file for some reason.

2. Try our development site (dev.glycam.org). There's a glycoprotein
builder there, too, and it is probably a lot faster and more robust
for the things it does. Please just be aware that the site is still
in development. The things that work should work properly, but some
functionality is missing. For example, you can't add counter-ions
yet. You should be able to build a glycoprotein, though. Of course,
always check your files carefully.

On Sun, Oct 14, 2012 at 10:59 PM, yanyuna<hiyanyuna.gmail.com> wrote:

Thank you very much.The following is what I have once asked and you have

" Have you tried using the online glycoprotein builder at glycam.org?
What you want to do is pretty difficult otherwise. That's why we
created the site.

On Sun, Oct 14, 2012 at 2:27 AM, yanyuna<hiyanyuna.gmail.com> wrote:
> Hi all,
> When I build the glycoprotein ,I build a glycan and I get a protein
> from the PDB bank.But I don't know how to align the CLYCAM-generated
> glycan with the protein and save the coordinates in a single file.
> Thanks in advance "
I have used the site you mentioned above,but I find it is so
slow.Whether I can minimize it myself to align them together,and if"

The pdb file is 1HNG.pdb . " RnCD2* were built by mutating Asp61 to
Thr61, Asn66 to Gln66, Asn76 to Gln76, and Asn83 to Asp83. These
mutations were introduced to ensure that the Asn-Gly-Thr
amino acid sequence was constructed and only one
glycosylation site was kept for RnCD2ad. The nonglycosylated
structure was obtained by simply removing the glycan from
glycosylated HsCD2ad(1GYA.pdb). The same glycan were also added to
Asn59 of RnCD2* to build the glycosylated RnCD2*. " Thank you

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Received on Mon Oct 15 2012 - 02:00:04 PDT
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