[AMBER] Forcefield for 5' phosphate in RNA

From: <dnlfr1994.gmail.com>
Date: Thu, 9 Jul 2020 14:01:36 +0200

Hi everyone,


I would like to ask if there is any working forcefield modification for
terminal 5’ phosphate nucleotides in RNA systems which is compatible with
the current OL3 forcefield.

I’ve looked for some info and I have only found an old (2003) issue in the
Amberlist Archive ( <http://ambermd.org/Questions/mail/251.html>
http://ambermd.org/Questions/mail/251.html) with an example for a guanine
with a terminal phosphate. I am wondering if using the parameters of this
example for a 5’p terminal uracyl would be suitable or not (although, I am
guessing it is not adequate).

I have also found other forcefield and prepi files in GitHub (
https://github.com/juvion/AmberFF_tRNA) which seem to be incompatible with
said forcefield.


I would be glad to hear any other suggestions if anyone knows a method to
successfully add a phosphate to a 5’ terminal ribonucleotide and perform the
MD simulation.


Thank you very much in advance,


Daniel Fernández


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Received on Thu Jul 09 2020 - 05:30:03 PDT
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