[AMBER] Capping RNA

From: Mihaljevic-Juric Paula (Mme) <paula.mihaljevic-juric.polytechnique.edu>
Date: Thu, 11 Apr 2019 11:56:08 +0200 (CEST)


I would like to use AMBER for RNA simulations. I am trying to convert CHARMM files to AMBER, so I am not sure which terminal patches to use in AMBER.

For example, if there are missing 5' and 3' terminal ends of the RNA, how should I cap it? In CHARMM I used 5PHO and 3PHO patches, as if I would have phospate groups with OH.

What would be the analogue to these terminal patches in AMBER?

Thank you

Have a great day

Paula Mihaljević-Jurič

PhD Student
BIOC, CNRS, École polytechnique
IP Paris, F-91128 Palaiseau, France

E-mail: [ mailto:paula.mihaljevic-juric.polytechnique.edu | paula.mihaljevic-juric.polytechnique.edu ] Tel: +385 95 368 4071

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Received on Thu Apr 11 2019 - 03:00:02 PDT
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