On Thu, Apr 5, 2012 at 9:58 AM, Vlad Cojocaru <
vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> Thanks David,
>
> This what I supposed. Just wanted to make sure I am right.
> Definitely, we will take a look at ff12SB as soon as we get hold of
> AMBER 12.
>
Another small detail -- you can download AmberTools 12 anytime (free),
which is the package that has all of the force fields.
HTH,
Jason
> Is fff12SB published already or in press ?
>
> Best,
> Vlad
>
> On 04/05/2012 03:53 PM, David A Case wrote:
> > On Thu, Apr 05, 2012, Vlad Cojocaru wrote:
> >> The aminoacids libraries for the ILDN modifications are in
> >> "all_amino94ildn.lib" (+ the nt and ct aa). So, I assumed that the file
> >> "all_aminont94.nmr.lib" should contain the corresponding libraries for
> >> the NMR-based modifications
> > No. Files like "all_amino94.nmr.lib" have nothing to do with the
> > Bruschweiler group modifications. These are ancient files originally
> used
> > for NMR refinements in gas-phase simulations. I've hesitated to delete
> > them, since refinement scripts still being used in NMR groups use them.
> >
> > The Bruschweiler files use the standard "94" lib files, parm99.dat, and a
> > special frcmod file: see the leaprc.ff99SBnmr file.
> >
> >> If we load "frcmod.ff99SB-ildn-nmr" (my modified version of frcmod as
> >> explained above) and "all_amino94ildn.lib" (+ nt and ct) are we sure to
> >> use the correct parameters for the NMR-based modifications of ff99SB ?
> > You should get in touch directly with Rafael to discuss this. But the
> only
> > files relating to the ff99SBnmr modifications are leaprc.ff99SBnmr and
> > frcmod.ff99SBnmr. Other files, that contain "nmr" but *not* "ff99SBnmr"
> are
> > used for different purposes.
> >
> > [As an aside, the Simmerling group has created ff12SB, which is
> certainly also
> > worth considering for protein simulations.]
> >
> > ....dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> --
> Dr. Vlad Cojocaru
> Max Planck Institute for Molecular Biomedicine
> Department of Cell and Developmental Biology
> Röntgenstrasse 20, 48149 Münster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Apr 05 2012 - 14:30:06 PDT
