Re: [AMBER] glyco

From: Lachele Foley (Lists) <"Lachele>
Date: Mon, 15 Oct 2012 20:26:50 -0400

On Mon, Oct 15, 2012 at 4:59 AM, yanyuna <> wrote:
> The pdb file is 1HNG.pdb .

I was just now able to successfully add a glycan to 1HNG.pdb. It took
a few minutes, maybe 5-ish, for it to build. But, seeing as how
that's a lot less time than waiting for me to respond, I'm guessing
you are having other trouble.

> " RnCD2* were built by mutating Asp61 to
> Thr61, Asn66 to Gln66, Asn76 to Gln76, and Asn83 to Asp83.

How did you perform the mutation? Did you just change the residue
name? Our software is very picky about what it is willing to build.
Each residue must contain only the correct atoms and no incorrect
ones. If you change the name of one residue to another, it is
probably safest to leave only the backbone atoms in place. The
software should rebuild the rest of the residue. If you want to leave
other atoms in for orientation purposes, make certain they have the
correct names and their geometries are appropriate. If you send me
the pdb file, I might be able to tell quickly what needs to be done.
I know it can be hard to tell sometimes.

> 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

I'm a bit lost here. You made a non-glycosylated structure from one
with a glycan (1GYA)? But, that was not appropriate to use for the
glycosylated structure, so you needed 1HNG for that? I don't need to
understand the details of your experiment, but I think I need more
information about what you are trying to build.

Some notes on 1GYA: (1) The old site ( will misbehave with
that file as-is. To use the old site you should choose one of the
solution-phase structures and remove the others from the file. You
should also remove the glycan. (2) If you use the new site
(, you should be able to leave the file as-is, except
that I found a bug in that builder just now. Assuming I fix that,
the glycan will not be recognized unless you rename it with our
residue and atom names.

I was able to build a glycoprotein on the old site with 1HNG as-is and
with 1GYA modified as mentioned just above. Each took a reasonable

:-) Lachele
Lachele Foley
Athens, GA USA
AMBER mailing list
Received on Mon Oct 15 2012 - 17:30:03 PDT
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