In connection with this note and the files that I have submitted about
these issues, I should remark that before running parmchk on the mol2
ff file (resulting in zero-periodicity around the new atom types), I
had run the frcmod file for the new atom types contained in the mol2
files. I had also added all atom types to the mol2 file.
thanks
francesco pietra
On Wed, Jul 25, 2012 at 9:06 PM, Jason Swails <jason.swails.gmail.com> wrote:
> 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
> _______________________________________________
> 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
Received on Wed Jul 25 2012 - 23:00:03 PDT
