Re: [AMBER] Forcefield for 5' phosphate in RNA

From: David A Case <>
Date: Thu, 9 Jul 2020 08:42:51 -0400

On Thu, Jul 09, 2020, 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
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