VMD-L Mailing List
From: Elena Lilkova (elilkova_at_phys.uni-sofia.bg)
Date: Tue Feb 17 2015 - 10:07:10 CST
OK, thanks for the information.
I read the FFTK paper and the description of "Scan Torsions" on the plugin
info site, but they says nothing about hydrogens :).
Maybe add this info to the FFTK plugin description site.
Thank You both again.
> 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
>> 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,
Atomic Physics Department,
Faculty of Physics,
University of Sofia "St. Kliment Ohridski"
5 James Bourchier Blvd.