Re: [AMBER] help, we are frequently face this error

From: David A Case <>
Date: Mon, 15 Nov 2021 15:37:02 -0500

On Mon, Nov 15, 2021, zeinab masoomi wrote:

>a structure is attached below, it's SARS-CoV-2 RBD glycosylated by glycam

It sounds like you should address this question to the people at GLYCAM.
Be sure to say exactly what you did (i.e. include your tleap script).
They may be have ideas about how to use this file in Amber. If you want to
re-post here, be sure to put "GLYCAM" in the subject line, so that Lachele
and GLYCAM folks will know to read the post.


>> >Could not find bond parameter for: OH - Cg

Maybe others on the list will recognize the issue here. You might have to
start with a very simple protein, with only one glycosylation site, in order
to get something easier to debug.

[Scott: does tleap know the atom numbers at the point where it prints the
above error message? That would be really helpful....]

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Received on Mon Nov 15 2021 - 13:00:03 PST
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