VMD-L Mailing List

From: Paweł Kędzierski (pawel.kedzierski_at_pwr.edu.pl)
Date: Tue Feb 20 2024 - 07:29:39 CST

W dniu 20.02.2024 o 13:09, Joel Subach pisze:
> Hello VMD Community in the above instance subsequent to the ffTK first
> tab blanks will be drawn for psf, par etc., accordingly working
> through all tabs depending will function best:).
Well, the parametrization procedure should in general follow the order
from Lennard-Jones through charges, bonding parameters then dihedrals,
since the latter depend on the former, and this is reflected by the
order of tabs in FFTK.

However, if your ligand is already properly parametrized then it does
make sense to only fix the penalized dihedrals. They are only
corrections to intramolecular interactions not sufficiently described by
other terms.

But the requirement is that you first convert all these external
parameters, topology and geometry to the formats required by FFTK, which
belongs to the CHARMM ecosystem, and use them as the starting point for
the calculation of the dihedral parameters. I know little about gromacs,
but I remember some subtle problems when I tried to use AMBER parameters
with VMD and NAMD tools, so there may be traps in such conversion. But
even if you parametrize your ligand in FFTK starting from scratch, then
you still will need to convert the full results - not just the dihedrals
- back to gromacs format anyway...
Pawel
>
> On Wed, Oct 18, 2023 at 1:13 PM Joel Subach <mjsubach_at_alumni.ncsu.edu>
> wrote:
>
> Hello VMD Community I hope you're well:).
>
> For the above topic I only need to optimize two-dihedral angles,
> can I therefore
> only select Scan and Opt Torsion tabs and ignore the others i.e.
> Opt Charge etc.?
> (My goal is to simulate a protein-ligand Complex via Gromacs and
> my ligand exhibited
> only two penalized dihedral angles needing optimization before
> proceeding any further.)
>
> Thanks if you know:) Joel 🚀
>