VMD-L Mailing List

From: Prof. Eddie (eackad_at_siue.edu)
Date: Sat Feb 06 2021 - 08:11:04 CST

Thank you. It seems my problem was that I was including all the target QM
data, not just the atoms I needed to optimize and that was giving me my
error.
Thanks for the workflow it is very helpful.
Best,
Eddie

On Wed, Feb 3, 2021 at 5:03 PM Daniel Fellner <dfel694_at_aucklanduni.ac.nz>
wrote:

> 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
>>
> 

-- 
_________________________________________________________
Edward Ackad, Ph.D <https://urldefense.com/v3/__http://www.siue.edu/*7Eeackad__;JQ!!DZ3fjg!tvmzB9-nOObEdAzC-n-4uuQAn-_y2X54hN-4PU0EG5A5MmXhtetmV30Rx3G4pmTVMw$ >
Associate Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390