From: Mayne, Christopher G (
Date: Tue Feb 17 2015 - 09:14:49 CST


Did the excluded dihedrals terminate in hydrogens?

ffTK's "Read from PAR" import button imports all dihedrals that don't terminate in hydrogen, as these are not typically scanned. Polar hydrogens are the exception, and should be added in manually.

Christopher Mayne

On Feb 17, 2015, at 7:46 AM, Elena Lilkova wrote:

> Dear FFTK experts,
> I have a question regarding the Scan Torsions section of FFTK. I would
> like to parameterize 14 diherdrals, that are all listed in my par file.
> When I use the "Read from PAR" button on the "Dihedrals to Scan" panel and
> load the par file, FFTK only lists 4 torsion angles. I do not understand
> why this is.
> When I use the file with the "Read from PAR" button on the "Dihedral
> Parameter Settings" of the "Opt. Torsions" section, all 14 dihedrals are
> listed correctly.
> I added manually the missing ten dihedrals for optimization, but I was
> wondering whether I am missing somthing here. I am supposed to generate
> gaussian input files for each of the diherals be parameterized, right?
> I am attaching my pdb, psf and par files.
> Elena Lilkova
> PhD student,
> Atomic Physics Department,
> Faculty of Physics,
> University of Sofia "St. Kliment Ohridski"
> 5 James Bourchier Blvd.
> 1164 Sofia,
> Bulgaria<model_charges.psf><opt.pdb><for_optimization_ba.par>