Re: [AMBER] Amber

From: David A Case <>
Date: Thu, 24 Mar 2011 11:34:47 -0400

On Thu, Mar 24, 2011, 姜笑楠 wrote:

> Firstly, I want to do the molecular dynamic simulation between RNA and
> its ligand, so I uploaded the complex of the RNA and the ligand. Using
> leaprc.ff03 force field, there is no corresponding parameters for
> U. How can I do? Choose another force filed, such as leaprc.rna.ff02?

Please read Chapter 2, "Specifying a force field" in the Users' Manual. ff03
is just a protein force field, so won't help for RNA. Your other suggestion,
leaprc.rna.ff02, is listed as an "obsolete force field" (Section 2.11) with
the note "we do *not* recommend that these be used any more for molecular

Choosing a force field is one of the most important aspects of carrying out
simulations. Please read Chapter 2 and literature examples with care. It is
likely that leaprc.ff99bsc0 is the best alternative among those currently in
Amber, but the field is still evolving:

  author = {Ban\'{a}\v{s}, P. and Hollas, D. and Zgarbov\'{a}, M. and Jurecka,
P. and Orozco, M. and Cheatham, III, T.E. and \v{S}poner, J. and Otyepka, M.},
  title = {{Performance of molecular mechanics force fields for RNA
simulations: Stability of UUCG and GNRA hairpins}},
  journal = {J. Chem. Theory. Comput.},
  volume = {6},
  pages = {3836-3849}
  year = {2010}


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