VMD-L Mailing List

From: Joel Subach (mjsubach_at_alumni.ncsu.edu)
Date: Tue Feb 20 2024 - 07:33:37 CST

Hello Pawel ok thank you for your kind update:).

On Tue, Feb 20, 2024 at 2:29 PM Paweł Kędzierski <
pawel.kedzierski_at_pwr.edu.pl> wrote:

> 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 🚀
>>
>
>