[AMBER] Glycosylation issue: Atom xx was assigned a lower molecule # than previous atom.

From: zizhang sheng <shengzizhang.gmail.com>
Date: Fri, 3 Jan 2020 16:44:04 -0500

Hi All,
I used Glycam website to add an MAN3 to my protein. I then renamed the ASN residue to NLN, and used teleap to generate topology and coordinate files. While teleap did not report any error, AMBER continue to report an error during MD (heating, equilibration, production): atom was assigned a lower molecule # than previous atom. If manually checking the structure, the atoms were assigned correctly. The atom in trouble is the C1 atom of 4YB. I attached the PDB files for teleap, the teleap script, and the generated top files. If using ambpdb to convert the topology file to pdb format, the same error occurs. But if I run MD on the protein without glycosylation, the MD run is good.
Hope you can help me figure out why this happens.


Zizhang Sheng

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Received on Fri Jan 03 2020 - 14:00:02 PST
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