[AMBER] RNA with 5' phosphates

From: Michael Bruist via AMBER <amber.ambermd.org>
Date: Mon, 5 Jun 2023 14:07:17 -0400

My group is trying to model RNAs with 5’-phosphates. We are getting crashes
that may indicate a problem for the force fields in terminalphos.lib
(Amber18) and terminalphos.LJbb-RNA (Amber20). Both have a problem in that
bond angles with the protonated oxygen are not maintained during
minimization or pmemd runs. See attached 10-frame movie for a failure in

Attached are the following files for our attempts to use this in AMBER20:

GMP_failure.mp4 a 10-frame movie showing the failure of the 5’ phosphate
in the upper left.

I also wanted to attach the parm file, but its size prohibited this
message from being accepted. I am including a link to a Google drive

For the future, what is the best way to provide access to such large files?

Thanks for your help.

Mike Bruist
Michael F. Bruist
Professor of Biochemistry
Department of Chemistry and Biochemistry
215-596-8530 (University City office)
610-649-5474 (home, "COVID office")

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Received on Mon Jun 05 2023 - 11:30:02 PDT
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