Re: [AMBER] using both the ILDN and NMR-based modifications of ff99SB

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Thu, 5 Apr 2012 11:07:21 -0400

it's not published yet, we have been making adjustments all the way up to
the release and are just getting it written up now.

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.
>
> 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
> >
> >
> > _______________________________________________
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> > 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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>
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Received on Thu Apr 05 2012 - 08:30:05 PDT
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