Re: [AMBER] PDB file carbohydrates naming problem

From: Rui Chen <>
Date: Tue, 20 Aug 2019 21:49:26 -0600

By the way, should I remove all the hydrogens before using PDB4AMBER and
why? Thank you.

On Tue, Aug 20, 2019 at 9:43 PM Rui Chen <> wrote:

> Hello,
> 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.
> Sincerely,
> Rui
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Received on Tue Aug 20 2019 - 21:00:03 PDT
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