Re: AMBER: CHARMM vs. AMBER ff literature

From: Jiri Sponer <>
Date: Thu, 12 Apr 2007 14:58:32 +0200 (MEST)

1) Regarding RNA.

AMBER works so far quite well, ca 5 microseconds of data
on systems ranging from A-RNA, through noncanonical helices,
folded systems like K-turns, several ribozymes, kiss complexes,
where detailed comparison with experiments was done.
It does not tell the ff is perfect, but it is meaningful and
often very useful. Most problems are expected for single
stranded loop topologies on longer time scales, no tests
published so far. As Tom Cheatham pointed out earlier.

Molecular dynamics simulations of RNA: An in silico single molecule approach
BIOPOLYMERS 85 (2): 169-184 FEB 5 2007

Other specific ff tests for nonWC pairing, tertiary interactions
as well as backbone families.
Cations and hydration in catalytic RNA: Molecular dynamics of the hepatitis delta virus ribozyme
BIOPHYSICAL JOURNAL 91 (2): 626-638 JUL 15 2006

Molecular dynamics simulations of sarcin-ricin rRNA motif
NUCLEIC ACIDS RESEARCH 34 (2): 697-708 2006

Structure, dynamics, and elasticity of free 16S rRNA helix 44 studied by molecular dynamics simulations
BIOPOLYMERS 82 (5): 504-520 AUG 5 2006

  CHARMM - basically, there are (to the best of my knowledge)
  no sufficient literature data
  for functional RNAs that would compare simulations with
  representative X-ray structures, one base pair after another.
  (Not just "RMSD was 4 A etc...", information of this kind tells nothing).
  Unless this is done nothing can be told about the charmm performance
  for RNA.
  Simulation of duplex RNA regions are not sufficient to assess the ff
  performance, RNAs are complex folded molecules.

  This paper (method section)
  Comparison of mode analyses at different resolutions applied to nucleic acid systems
  Author(s): Van Wynsberghe AW, Cui Q
  Source: BIOPHYSICAL JOURNAL 89 (5): 2939-2949 NOV 2005
  reports "instability" for charmm trajectory on a folded
  ribozyme, but no details are given (there is just one
  sentence in the paper) and the authors subsequently
  switched to AMBER.

2) DNA, as Tom Cheatham pointed out, the current status is given in

  Best wishes, Jiri

Jiri Sponer
Academy of Sciences of the Czech Republic
Kralovopolska 135
CZ-61265 Brno
Czech Republic
fax: 420 5412 12179
phone: 420 5415 17133
Senior Wellcome Trust International Research Fellow for Biomedical Science

[ Charset ISO-8859-1 unsupported, converting... ]
> Dear Amber Users,
> Is there a good paper or link someone can point me to that describes the major
> differences between CHARMM and AMBER Force Fields as they apply to nucleic
> acids?
> Thanks,
> Seth
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Received on Sun Apr 15 2007 - 06:07:19 PDT
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