R.E.D. Server: Test case

The generation of a force field topology database (FFTopDB) in the Tripos mol3 file format as well as force field parameters for ten solvent molecules is presented in these demonstration pages. The data obtained correspond to the W-46 R.E.DD.B. project. At the end of a R.E.D. Server job, a Jmol based graphical interface is generated allowing the user to display, study and download the data generated (see FAQ 1). The corresponding files are kept available for five days on the R.E.D. Server hard drives (see FAQ 11). Another example related to empirical force field construction for regular deoxyribonucleic acid is available here.

Execution of PyRED: direct empirical force field generation from a list of PDB files
Errors have been volontary incorporated into the PDB input files to highlight automatic corrections carried out by the PyRED program.

PDB files(s)	Molecule name
Display the local file 1	Dimethylsulfoxide
Display the local file 2	Ethanol
Display the local file 3	Trifluoroethanol
Display the local file 4	Methanol
Display the local file 5	Acetone
Display the local file 6	Acetic acid
Display the local file 7	Acetonitrile
Display the local file 8	Benzene
Display the local file 9	Toluene
Display the local file 10	Chloroform

QM output(s)	Molecule name
Display the local file 1 (reduced size)	Dimethylsulfoxide
Display the local file 2 (reduced size)	Ethanol
Display the local file 3 (reduced size)	Trifluoroethanol
Display the local file 4 (reduced size)	Methanol
Display the local file 5 (reduced size)	Acetone
Display the local file 6 (reduced size)	Acetic acid
Display the local file 7 (reduced size)	Acetonitrile
Display the local file 8 (reduced size)	Benzene
Display the local file 9 (reduced size)	Toluene
Display the local file 10 (reduced size)	Chloroform

The following Project.config, System.config and frcmod.user files are also used in this demonstration (see the readme.txt file).