On Thu, Jul 09, 2020, dnlfr1994.gmail.com wrote:
>
>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.
Yes: look at $AMBERHOME/dat/leap/lib/terminal_monophosphate.lib. You would
typically use loadOff in tleap to load this (after sourcing leaprc.RNA.OL3).
Somehow, this information didn't make it into the Amber 2020 Reference Manual:
I'll get that fixed. Note that this library assumes that the terminal
phosphate is singly-protonated. That is not always the right choice, but we
don't have pre-built residues for other protonation options.
...good luck...dac
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Received on Thu Jul 09 2020 - 06:00:06 PDT
