Re: [AMBER] Glycan naming problem

From: Dr. Anselm Horn <>
Date: Thu, 4 Jul 2019 13:42:37 +0200

Hello Rui,

to learn the atom names of the specific glycans, you may use xleap:

After sourcing the glycam force field, use the edit command to visualize
the 3D structure of the carbohydrate of interest in a separate window
and then have its atom names depicted via "Display" -> "Names". This
should enable you to find the corresponding atom names for manual
substitution in your input pdb file.



> 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,
> Rui
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Received on Thu Jul 04 2019 - 05:00:02 PDT
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