RNA force field for AMBER
Reparameterized glycosidic torsion for RNA
We have developed new parameters for glycosidic torsion in RNA [Banas et al., 2010] for AMBER. This reparameterization [Zgarbova et al., in press] prevents formation of the degrading "ladder-like" structures of RNA [Mlynsky et al., 2010] and improves description of the syn region [Banas et al., 2010]. It seems that the best performance is achieved in combination with the bsc0 parameters (improving alpha/gamma torsion profiles) [Perez et al., 2007], but the reparameterized chi torsion can also be combined with standard parm99 force field. The adjusted parameters do not improve behavior of DNA simulations. The parameters are involved in the recent AMBER ff10 force field.
Parameters
Here are links to zipped files: ff99bsc0XOL, ff99XOL .
In the zipped files above (or in the following links) you can find two prep files
all_nuc94_ol_bsc0.in, all_nuc94_ol.in
corresponding to ff99bsc0XOL, ff99XOL force field, respectively, and parameter file frcmod.ol.dat with non-standard parameters.
How to use parmbsc0chiOL (parmbsc0XOL)
The combination of parmbsc0 with reparameterized chi torsion seems to perform best, so we recommend to use the ff99bsc0XOL variant.
You should upload standard force field ff99bsc0 to Leap program as usually and then overwrite the
standard all_nuc94.lib prep library by all_nuc94_ol_bsc0.in
and extend parm99.dat parameter file by frcmod.ol.dat.
Here is an example of Leap commands to use ff99bsc0XOL force field:
source $AMBERHOME/dat/leap/cmd/leaprc.ff99bsc0
loadamberprep all_nuc94_ol_bsc0.in
loadamberparams frcmod.ol.dat
Note that both non-standard prep file (e.g., all_nuc94_ol_bsc0.in) and additional parameters (e.g.,
frcmod.ol.dat) should be placed in current directory, from which Leap was launched or you
should define the path to these files in Leap using command "AddPath".
References
- Banas P,Hollas D, Zgarbova M, Jurecka P, Orozco M, Cheatham T, Sponer J, Otyepka M: Performance of Molecular Mechanics Force Fields for RNA Simulations. Stability of UUCG and GNRA hairpins. J. Chem. Theor. Comput, 6(12), 3836-3849, 2010 (Am. Chem. Soc.)
- Mlynsky V, Banas P, Hollas D, Reblova K, Walter NG, Sponer J, Otyepka M: Extensive Molecular Dynamics Simulations Show That Canonical G8 and Protonated A38H+ Forms Are Most Consistent with Crystal Structures of Hairpin Ribozyme. J. Phys. Chem. B, 114(19), 6642-6652, 2010 (Am. Chem. Soc.)
- Perez A, Marchan I, Svozil D, Sponer J, Cheatham TE, Laughton CA, Orozco M: Refinenement of the AMBER force field for nucleic acids: Improving the description of alpha/gamma conformers. Biophys. J. 92(11), 3817-3829, 2007
- Zgarbova M, Otyepka M, Sponer J, Mladek A, Banas P, Cheatham TE, Jurecka P: Refinement of the Cornell et al. Nucleic Acids Force Field based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles. J. Chem. Theor. Comput, in press, 2011