On Tue, 2014-10-28 at 16:12 +0100, Vlad Cojocaru wrote:
> Dear all,
>
> We are now starting some simulations with the new force field
> recommendations as of AMBER14 ...
> In the manual it is written that the RNA force field included in ff14SB
> is ff99+bsc0+chiOL3 .... First, I also believe it is an unfortunate
> confusion to include nucleic acids force fields under the name "ff14SB"
> which is a protein force field.
I think this could be the inertial remnants of a time when protein and
nucleic acid force field development was not so specialized, such that
they were more or less developed together.
I can understand the initial confusion, although hopefully it isn't too
difficult to find the required clarity in the documentation.
> Second, I am confused because while the chiOL3 modifications are
> included in parm10.dat file, the nucleic12.lib library which is loaded
> in the leaprc.ff14SB file does not appear to contain any RNA units ....
> Is the "RNA_CI.lib", the correct RNA library to load ?
No. The PDB residue naming standards changed a few years ago. RNA
residues are no longer prefixed with "R", but instead have the bare
letters. So instead of RA, RG, RC, and RU the residues are named A, G,
C, and U.
If you look in nucleic12.lib, you will see those residues are defined.
Furthermore, if you look at the addPdbResMap command in the
leaprc.ff14SB file, you will also find that we attempt to support the
old RNA PDB naming scheme by mapping residue names RA to A, RC to C, RG
to G, and RU to U.
I hope this helped,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Oct 28 2014 - 09:00:02 PDT
