I do not know what the special characters are in your titles there. I have
listed for you the nucleic acid force fields that Amber offers as part of
its installation--OL15 is among them but I do not know about the ff99bsc
model. I have heard of something like this but you will need to look in
the directories I described to see if there are perhaps some hints in the
comments of those files. In leaprc.DNA.OL15, the preamble states:
#
# ----- NOTE: this is designed for PDB format 3!
# Uses ff99bsc0+OL15 for DNA
# (ff99): Wang et al. J. Comp. Chem. 21: 1049, 2000
# (bsc0): Perez et al. Biophys J. 92: 3817, 2007
# (OL15): Zgarbova et al. JCTC 11: 5723, 2015
# load atom type hybridizations
#
So there is definitely a component of ff99bsc0 in there, but I don't know
about the OL1 part you are talking about.
Dave
On Thu, Sep 17, 2020 at 12:15 AM Jenny 148 <jenny.rs140.gmail.com> wrote:
> Sir,
> My major doubt is whether OL15 forcefield and ff99bsc0εζ OL1 forcefield are
> the same??
> On 17 Sep 2020 09:05, "David Cerutti" <dscerutti.gmail.com> wrote:
>
> > In order to source a nucleic acids force field you will state, in your
> > leaprc, things like this:
> >
> > source leaprc.DNA.OL15
> > source leaprc.RNA.OL3
> >
> > For DNA< you have choices of bsc1 and OL15--I am almost certain that
> those
> > are substantially different, but check the literature from Cheatham
> group.
> > For RNA, you have LJbb, OL3, ROC, Shaw, and YIL options. I cannot advise
> > you on one model or another in this respect, but look in each of the
> leaprc
> > files (located in ${AMBERHOME}/dat/leap/cmd/leaprc.[RD]NA.(option), and
> > you
> > should see lines like "loadOff DNA.OL15.lib" and "parm10 =
> loadAmberParams
> > parm10.dat." The latter tells it to use torsion parameters from parm10, a
> > central collection of valence terms from our protein force fields. You
> > will find parm##.dat files in ${AMBERHOME}/dat/leap/parm/, and .lib
> > (library) files in ${AMBERHOME}/dat/leap/lib/.
> >
> > HTH,
> > Dave
> >
> >
> > On Wed, Sep 16, 2020 at 9:12 AM Jenny 148 <jenny.rs140.gmail.com> wrote:
> >
> > > Dear all,
> > > The question might be really trivial. I would like to know if the OL15
> > > forcefield and ff99bsc0εζ OL1 forcefield are the same. If not what is
> the
> > > difference. And how to source ff99bsc0εζ OL1? Thank you for your
> time.
> > >
> > > --
> > > Jenny R.S
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Wed Sep 16 2020 - 21:30:03 PDT
