Hello everyone,
we are performing calculations with AMBER8 on short glycoproteins (34 residues) containing a GlcNAc linked to Asn.
We have built this Asn(GlcNAc) using GLYCAM and the formatting tools provided on the
http://glycam.ccrc.uga.edu website, and everything works very nice.
Our observation, however, is that in the 20 .pdb output structures the two carbon-proton bonds at the C6 of GlcNAc are broken. One of the two protons always ends up nonbonded, approx. 4-6 angstroms away from the sugar, while the other proton always gets bonded to a residue neighboring the Asn(GlcNAc) (for example, the adjacent Phe amide becomes - CO-NH2 - ).
In the other 20 output structures (.rot.pdb), however, everything is fine.
If we run the cleanup script after the calculations, this error is indicated as RMS deviations for the ensemble (GlcNAc is named 0YB, and has residue number 34):
**** Error in coords for atom: 1H6- 0Y- 34
**** Error in coords for atom: 2H6- 0Y- 34
(this message appears once for every .pdf created)
We do not know whether this is a common problem when the program tries to handle glycosylated residues, and maybe this problem has been observed before?
Thank you for your suggestions,
Sebastian Enck
__________________________
Sebastian Enck, Ph.D.
The Scripps Research Institute
Beckman Center
10550 North Torrey Pines Road
La Jolla, CA 92037
encks.scripps.edu
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Received on Tue Feb 14 2012 - 09:30:02 PST
