Application to charge derivation, force field library building and force field parameter generation
F. Wang
Université de Picardie - Jules Verne, Amiens
J.-P. Becker
Université de Picardie - Jules Verne, Amiens
P. Cieplak
Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
F.-Y. Dupradeau *
Université de Picardie - Jules Verne, Amiens
December 3rd, 2021
Section "-II.4- A metal complex": add a remark about element radii used in MEP computation.
November 20th, 2021
Section "-II.4- A metal complex": add two remarks to differentiate covalently bound-cobalt(III) and ionically-bound-cobalt(III) complexes.
November 22nd, 2021
Slightly adapt the PDB input file format used by PyRED.
August 6th, 2022
Add new remarks in the "-V.3- Force field for a set of nucleotide fragments" section
August 24th, 2022
Add new remarks in the "-V.2- Force field for a set of amino acid fragments" section
Add new JSmol applets to graphically display the molecules of this tutorial
Add a new section entitled: 'Biopolymer and macrostructure construction from molecular fragments within the LEaP program'
Update: 'https://upjv.q4md-forcefieldtools.org/Tutorial/Tutorial-4-demo5.pdf'
Update: 'https://upjv.q4md-forcefieldtools.org/Tutorial/Tutorial-4-demo6.pdf'
September 4th, 2022
Replace gif images by more informative svg images
October 15th, 2022
New tutorial part entitled: 'Working with a 'large' input molecule/polymer with R.E.D.Server Develoment/PyRED and LEaP'
A new JSmol applet for the part entitled: '-II- Empirical force field generation for a single molecule'
Better define the importance of the molecular conformation in the part entitled: '-II- Empirical force field generation for a single molecule
June 30th, 2023
Updates of text and add new web links.
September 4th, 2023
Correct typos in the Project.config files in the -II.4- section
September 14th, 2023
New tutorial part entitled: 'Preparing the input molecule(s) for R.E.D. Server Develoment/PyRED'
Should you find any mistake in this tutorial, please, send me an e-mail:
If you have questions about this tutorial, please, send your emails to the q4md-forcefieldtools mailing list. We will answer to the queries about the q4md-forcefield tools in the Amber or CCL mailing lists as well.
Last update of this tutorial page: September 16th, 2024.
Charge derivation data free for download.
Université de Picardie Jules Verne. Sanford Burnham Prebys Medical Discovery Institute.
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