AMBER Archive (2008)

Subject: AMBER: Glycoprotein once again..........

From: dipti lele (
Date: Thu Aug 14 2008 - 07:10:10 CDT

Hello All,

    As per the manual I have tried to build a glycoprotein. I have used
Glycam online server to generate the glycan aligned to the protein surface.
I have also changed the names of the residues like thr to OLT etc. Then I
used the bond command to generate a bond between two atoms as per the
requirement. It did not show any warning further neither any error. Then I
made a topology file and parameter file. After the energy minimisation once
again the bond between the protein and carbohydrate was found to be broken.
Is there anything else I need to do regarding it. Probably a step in between
which I have missed. Or some basic mistake which I am doing???

Thanks a lot

Deepti Lele,
NII, New Delhi.

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