Re: [AMBER] Phosphorylated-RNA

From: Thomas Cheatham <>
Date: Mon, 9 May 2016 20:11:30 -0600 (MDT)

> I am trying to conduct a molecular dynamics about a RNA-protein complex.
> My problem is that the RA5 in the RNA structure is phosphorylated and
> Leap cannot recognise it. What should I do to solve the problem?

Either remove the terminal phosphate or develop new parameters with the
terminal phosphate. It would likely be much easier to remove the
phosphate, unless of course the terminal phosphate is critical for
whatever property you are interested in (structure, dynamics, catalysis,


AMBER mailing list
Received on Mon May 09 2016 - 19:30:03 PDT
Custom Search