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
minimization.
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.
tleap_commands.txt
TLS1_clipped_K.inmin
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
folder.
https://drive.google.com/drive/folders/1EvhLYvcV5DkpDGNmbQR7B5-R8Pd_yeTp?usp=sharing
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
