VMD-L Mailing List
From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Tue Feb 17 2015 - 08:50:02 CST
FFTK by default only scans non-redundant torsions. For instance in
ethanol, there are many dihedral terms to parameterize (2 from the
carbon-oxygen bond and 2 from the carbon-carbon bond), but only 2
rotateable bonds to "scan". FFTK in this case will only scan two
torsions, one from each rotateable bond. You compound probably has the
same thing going on. You can always add more torsions to scan on your
own if you think its missing something.
On 02/17/2015 07:46 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,