Re: [AMBER] Regarding DNA forcefield in Amber14

From: Mahad Gatti Iou <>
Date: Wed, 5 Aug 2015 14:47:30 +0200

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:
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
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.


2015-08-05 10:40 GMT+02:00 Vlad Cojocaru <>

> 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]
> _______________________________________________
> AMBER mailing list
AMBER mailing list
Received on Wed Aug 05 2015 - 06:00:11 PDT
Custom Search