On Mon, Feb 29, 2016, Jason Swails wrote:
>
> The bug is reported here: https://github.com/choderalab/openmm/issues/12
>
> An example of the issue are lines 64 and 121:
> CA-N2 449 1.349 same as ca-nh
> N2-CA 449 1.363 same as ca-nh
>
> umm.... ? Where did this file come from? It's clearly not right.
>From the SantaLucia group (I think from their website). See the top of the
leaprc.modrna08 file:
#
# ----- leaprc for loading modified RNA nucleotides. The parameters are
# described here:
# R. Aduri, B.T. Psciuk, P. Saro, H. Taniga,
# Schlegel, H.B. and J. SantaLucia, Jr. AMBER force field parameters
# for the naturally occurring modified nucleosides in RNA.
# J. Chem. Theory Comput. 3, 1465-1475, 2007.
#
# To use these residues, load this file into leap, after the Amber-FF, e.g.:
#
# > source leaprc.ff14SB
# > source leaprc.modrna08
#
modrna08 = loadAmberParams all_modrna08.frcmod
loadOff all_modrna08.lib
Note that the file name in the Amber distribution is different than the one
you cite, but the bug is the same. The original web site that had these
(ozone3.chem.wayne.edu) appears to have moved (or been removed).
...dac
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Tue Mar 01 2016 - 06:30:03 PST
