VMD-L Mailing List

From: Daniel Fellner (dfel694_at_aucklanduni.ac.nz)
Date: Wed Feb 03 2021 - 17:02:50 CST

Best practice is to utilise any existing parameters (via CGenFF) and only
optimise what is necessary. For small molecules I recommend the following
procedure:

1. Create a .mol2 file compatible with CGenFF (paramchem.org) – I recommend
using the attached format. You can manually edit your noncompliant .mol2
files with Notepad++ or Vim to match this. Choose any 3-character
identifier for the header and last column.
2. After making an account on paramchem.org, upload the .mol2 file leaving
all options as default. Download the resulting .str file and inspect the
charge and parameter penalties. Penalties over 50 mandate optimisation, so
make a mental note of the charges, bonds, angles, and dihedrals with
penalties you think require manual parameterisation.
3. Using the "Prepare Parameterization from CGenFF Program Output" tab,
generate your initial PSF/PDB/PAR files from the .mol2 and .str file.
4. Proceed to Opt. Geom, Charge Opt. etc.
5. Once you're finished, you'll have to merge your final par file with the
prm and top files (or is it just top?) generated by CHARMM-GUI for a
complete set of parameters.

*Daniel Fellner BSc(Hons)*
PhD Candidate
School of Chemical Sciences
University of Auckland
Ph +64211605326

On Thu, Feb 4, 2021 at 5:31 AM Prof. Eddie <eackad_at_siue.edu> wrote:

> Hi all,
> I wanted to try and optimize progesterone (for use and to learn more about
> parameterization) using fftk so I started by using the charmmgui ligand
> reader on progesterone and then used the pdb and psf to start fftk. The
> problem is once I get to the Opt. Charg. it gives the error: domain error:
> argument not in a valid range for the ComputerIntE line 47 (and the formula
> looks like the vdW formula). I notice when I put in the charmmgui generated
> psd/pdb and all the parameter files (toppar/par_all36* ) fftk comes up
> empty for the VDW/LJ parameters. The existing and analogy prm files don't
> have anything in them for vdw. Is there some missing step I need to do
> since it doesn't find any missing vdw/LJ?
> Thanks,
> Eddie
>
> --
> _________________________________________________________
> Edward Ackad, Ph.D
> <https://urldefense.com/v3/__http://www.siue.edu/*7Eeackad__;JQ!!DZ3fjg!v6F9N0dL5QDuW3JgtRi4AMWrPMH0uHhPYI32wku80GV0r6GMtVdwMVlfpC8Xq_lehQ$>
> Associate Professor of Physics
> Computational Nanophotonics
> Southern Illinois University Edwardsville
> (618) 650-2390
>