Dear Vlad,
are you sure that you need to use ff99SB for RNA? I mean, when loading the
ff14SB using leap this is the output:
Welcome to LEaP!
Sourcing: /home/mgatti/Scrivania/amber14/dat/leap/cmd/leaprc.ff14SB
Log file: ./leap.log
Loading parameters: /home/mgatti/Scrivania/amber14/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters:
/home/mgatti/Scrivania/amber14/dat/leap/parm/frcmod.ff14SB
Reading force field modification type file (frcmod)
Reading title:
ff14SB protein backbone and sidechain parameters
Loading library: /home/mgatti/Scrivania/amber14/dat/leap/lib/amino12.lib
Loading library: /home/mgatti/Scrivania/amber14/dat/leap/lib/aminoct12.lib
Loading library: /home/mgatti/Scrivania/amber14/dat/leap/lib/aminont12.lib
Loading library: /home/mgatti/Scrivania/amber14/dat/leap/lib/nucleic12.lib
Loading library: /home/mgatti/Scrivania/amber14/dat/leap/lib/atomic_ions.lib
Loading library: /home/mgatti/Scrivania/amber14/dat/leap/lib/solvents.lib
It seems that is loading everything. I knew that with this you can use it
for both protein as well as RNA/DNA since, for instance, I have to analyze
a protein-nucleic acids complex so I need both force fields.
Maybe the ff99SB is useful if you have to simulate only a DNA/RNA molecule
but if it is in complex with amino acids I think it should do the trick
using the last ones no?
For me at least the simulations are going properly, pointing out that
nucleic acids simulations are tough.
Also I found this just by typing "amber rna force field" on google
(website: http://fch.upol.cz/en/ff_ol/index.php)
Force Field for RNA
We recommend ff99bsc0χOL3 combination which is well tested. This is
basically ff99 force field [4] combined with Barcelona bsc0 correction for
α/γ backbone torsions [5] and a χOL3(= χOL) correction for the glycosidic
torsion [6,7] which prevents formation of spurious "ladder like" structures
[6,8]. This combination is present in the ff10, ff12SB and ff14SB force
fields and is assigned by default by AmberTools 12, 13, 14 and 15 with its
LEaP based tools.
Cheers,
Mahad
2015-08-05 10:40 GMT+02:00 Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>
:
> By the way, ... because this confusion comes up pretty often and
> unfortunately it is also in the AMBER manual ...
>
> I'd like to stress that "ff14SB" is a pure protein force field (see
> recent papers from Carlos Simmerling's lab).
>
> For DNA the force field is "ff99+bsc0" (the one you used) or adding the
> latest modifications "ff99+bsc0+epsOL1+chiOL4" (see table 3.2 in the
> AMBER15 manual).
>
> The confusion comes up because the leap files used to load the ff14SB
> force field (leaprc.ff14SB, parameter and library files) already contain
> the bsc0 modifications for DNA ...
>
> Vlad
>
> On 08/05/2015 10:25 AM, Vlad Cojocaru wrote:
> > Dear Pragya,
> >
> > If you want to continue a previous study (restart a previous
> > simulation or run a new simulation for direct comparison with previous
> > one), the best is to use exactly the same force fields you used
> > before. Well, unless your precise goal is to compare different force
> > fields which is a different issue ...
> >
> > Those force fields you used provide already pretty good description
> > for lots of properties. Although, it always depends what you are after
> > so its impossible to say if the force fields were good enough for your
> > question unless we know the question.
> >
> > However, if you want to start a new study, then you probably also want
> > to make use of the latest developments and especially improvements for
> > your particular problem. The AMBER15 manual has a comprehensive
> > description of new force fields for different biomolecules at pages
> > 30-40. I think if you read those pages plus if you read the literature
> > where the modifications were published you should get a good idea how
> > to choose your force field.
> >
> > Best wishes
> > Vlad
> >
> > On 08/05/2015 09:35 AM, Pragya Priyadarshini wrote:
> >>
> >> Dear Amber users,
> >>
> >> I have to do MD simulation of protein-DNA complex, earlier I have used
> >> ff99SB + bsc0 force field of AMBER11, now I have to use AMBER 14 for my
> >> study. For protein, it is mentioned in AMBER14 manual, to use ff14SB but
> >> I am not getting about DNA. Is ff14SB, sufficient for DNA of protein-DNA
> >> complex or I have to other force field.
> >>
> >> Please suggest me.
> >>
> >> Regards
> >>
> >
>
> --
> 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/43241/cojocaru
>
>
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Received on Wed Aug 05 2015 - 06:00:11 PDT
