R.E.D. Server Development - Performing calculations with the PyRED program:
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 entitledi: '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




Waiting for the first report...
Date: Description of the problem: Location in the Tutorial



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Release of this tutorial: May 1st, 2014.
Last update of this tutorial page: October 17th, 2022.

Charge derivation data free for download.
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