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
>
>
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--
==========================================
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
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Received on Wed Jul 25 2012 - 10:00:04 PDT
