Hi!
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 11 2019 - 03:00:02 PDT
