Are you talking about pdb structures downloaded from our website, or
the output of a simulation or something else? Have you loaded
corresponding topology and restart/trajectory files? PDB displays
often "bond by distance." It's important to know what the topology
thinks is bonded. If you've loaded the top/crd, how did they look?
On Tue, Feb 14, 2012 at 12:09 PM, Sebastian Enck <encks.scripps.edu> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 14 2012 - 10:30:02 PST
