[AMBER] Glycan naming problem

From: Rui Chen <rchen6.ualberta.ca>
Date: Wed, 3 Jul 2019 22:28:32 -0600


I added glycans to a protein using CHARMM GUI, because when I used GLYCAM,
the glycans I added have severe steric clashes.

However, CHARMM GUI and GLYCAM have different naming format. In order to
use LEaP to prepare the glycoprotein to do MD simulation, I almost manually
modified all the differences, except for the H2N, C2N, O2N and CME. I
could't find the meaning of these specific atom types. Because it seems
like LEaP doesn't understand the pdb file generated by CHARMM GUI.

How can I solve the problem?

Looking forward to your reply.

Best regards,
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Received on Wed Jul 03 2019 - 21:30:02 PDT
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