Hello,
As a note, you should *always* inspect the frcmod file printed out by
parmchk. In it, you will see lines like:
C -H 0.00 0.000 ATTN, need revision
in the 'bond' section and
C -C -O -C 1 0.000 0.000 0.000 ATTN, need
revision
in the dihedral section. The string "ATTN, need revision" indicates that
parmchk could not figure out what the parameters should be, so it put 0's
in every position as place holders. You then have to go back and manually
fix those.
This is expected and documented behavior for parmchk -- see pps. 97-98 of
the AmberTools 12 manual for a clear description of the exact problem you
are seeing.
HTH,
Jason
On Wed, Jul 25, 2012 at 12:56 PM, Lorenzo Gontrani <l.gontrani.caspur.it>wrote:
> Dear Amber fellows, following the discussion on dihedrals with zero
> periodicity, I would like to report that I got the same type of
> problem after a parameter optimization run with paramfit (ambertools
> 12).
> Starting from a gaff-type force field, with all dihedrals with correct
> periodicity (non-zero), two dihedrals were assigned a zero periodicity
> after the GA fitting of ab initio potential energy surface.
> I gave no importance to this fact, when I ran the simulation
> afterwards (the trajectory was in better agreement with experiment),
> but I must admit that I used it as a "black box". Probably, the most
> important improvement occured for stretching and bending terms. Apart
> from the fit, a zero-fold periodicity corresponds to a constant term
> added to the force field, am I right?
> I am even starting to prepare an article to report the "success" of
> paramfit procedure, but I am now wondering if it is worth or not..
>
> Lorenzo
>
>
> 2012/7/24 David A. Case <case.biomaps.rutgers.edu>:
> > On Tue, Jul 24, 2012, Francesco Pietra wrote:
> >
> > Jason wrote:
> >> > However, can you tell what dihedral has periodicity 0 and where that
> >> > parameter comes from? It seems like that parameter file should be
> changed,
> >> > wherever it is.
> >>
> >> The only additional params are in a file creating new atom types for
> >> the olefinic carbons in the inserted lipid (trans enone)....
> >>
> >> Additionally, with parmchk I created a frcmod file from the mol2 ff
> >> file for the ensemble of aa inglobating the enone.
> >
> > So, does the output of parmchk have the zero-periodicity torsion? If
> so, it's
> > a bug and we can try to track it down, especially if you can come up
> with a
> > simple example where parmchk gives bad results; (info about what charge
> model
> > was used, etc, are not relevant here.)
> >
> > If it's not parmchk that is creating the problem dihedral, it would be
> good
> > to try to figure out where else it might be coming from.
> >
> > ...thx...dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> ==========================================
> Lorenzo Gontrani
> Research associate of CNR-ISTM (Rome Tor Vergata)
> EDXD group of University of Rome "La Sapienza"
>
> GSM +39 338 7615798
> Email l DOT gontrani AT caspur DOT it
> Webpage: http://webcaminiti/gontrani.html
> =========================================
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> 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 Wed Jul 25 2012 - 12:30:03 PDT
