Thanks a lot ,
My mistake .. I should have noticed the removal of the "R" for RNA
residues ... Although, personally I liked the "R" ...
Best,
Vlad
On 10/28/2014 04:36 PM, Jason Swails wrote:
> 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
>
--
Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
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Received on Tue Oct 28 2014 - 09:00:03 PDT
