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Hi Oliver and Lachele,

Thanks for your reply. My "pentamer" is a heteromer which is consisted of two identical heterodimers and one monomer. They are not bonded covalently but through van der Waal's interaction. I managed to solve it by appending TER between each monomer. Now Glycam server can recognize them perfectly. 

Regards,
Simon Kit Sang Chu
Ph.D. student
Biophysics Graduate Group
University of California Davis


On Mon, Nov 5, 2018 at 5:16 AM Oliver Grant <[log in to unmask]> wrote:
If I interpreted correct, perhaps protomer is the word to use instead of peptide. In a PDB file sometimes each protomer of an oligomer will have MODEL and END cards between each protomer. Try removing them. You can also load the PDB file into something like USCF Chimera and rename the chains and/or renumber the residues to be contiguous. 

If you can't get it to work, write us again. If you can provide the PDB ID for your system that would be useful.

Best,
Oliver


On Mon, Nov 5, 2018 at 1:52 PM Lachele Foley <[log in to unmask]> wrote:
We need some clarification.  Is the pentamer you speak of a peptide made of five amino acids?  If not that, then please specify.  

If you want to attach a glycan to a single, zwitterionic, amino acid, GLYCAM has, available for this purpose, variants of serine and threonine (residue names ZOLS and ZOLT).  If you want to model any other amino acids, or if you don't want the zwitterionic form, you will need to generate a residue with partial atomic charges.

Our server will only detect that two cysteine residues are capable of forming a disulfide bond if their sulfur atoms are proximal.  For this to happen, your peptide will need to be uploaded in a conformation where that is the case.  

If none of what I just said answers your questions, then I didn't understand your situation.  


On Sun, Nov 4, 2018 at 1:26 AM Kit Sang Chu <[log in to unmask]> wrote:
Dear users of Glycam,

I am a new user to Glycam and I am trying to build glycoprotein by submitting a pentamer on Glycam server. However, Glycam only recognizes one peptide with two terminals. Is there any specification on how Glycam server recognizes monomer units? 

I also need disulfide bonds built. Submitting a pentamer directly will therefore make things much more convenient.

Regards,
Simon Kit Sang Chu
Ph.D. student
Biophysics Graduate Group
University of California Davis


--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA