[AMBER] PDB file carbohydrates naming problem

From: Rui Chen <rchen6.ualberta.ca>
Date: Tue, 20 Aug 2019 21:43:45 -0600


I am preparing a PDB file for running LEaP. Since I add glycans using
CHARMM GUI, I rename the glycans to NLN (N-linkages to ASN) according to
AMBER manual (LEaP). However, I got error when I run leap. I changed the
TER cards, but it still didn't work. I also checked the connections between
the carbohydrates and the ASN amino acids using VMD, I couldn't find
anything wrong. The leap input file, log file, pdb file (mentioned in leap
input file) are attached.

Could you please give me some clue about how to solve the problem? Looking
forward to hearing from you.


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Received on Tue Aug 20 2019 - 21:00:02 PDT
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