FF: force field
R.E.D. Server Development is open to all users.
See the documentation and Frequently Asked Questions.
| Features related to the PyRED program |
| FF: Force field; FFTopDB: FF Topology DataBase; QM: quantum mechanics; MEP: Molecular electroctatic potential; MM: molecular mechanics |
| * Main steps carried out by PyRED |
| It handles complex approaches involving multiple molecules, conformations and orientations |
| - Step 1: Geometry optimization using QM |
| - Step 2: MEP computation using QM |
| - Step 3: Charge fitting, FF library & FF parameter generation |
| * Control of the input molecules |
| - Use the Protein Data Bank file format |
| - Determination of molecular topology |
| - Definition of chemical equivalencing |
| - Control/correction of atom names |
| - Control/correction of residue names |
| - Control of all the elements of the periodic table |
| - Control/modification of the atom order |
| * QM Computation |
| - Default approach: geometry optimization & MEP computation |
| - Complex approach: geometry optimization, MEP & frequency computation, wavefunction stability |
| - Pre-defined and user-defined options |
| - Compatibility with all the elements of the periodic table |
| * Charge derivation |
| - Control of molecular orientation before MEP computation |
| - Reproducible charge values |
| - Pre-defined and user-defined ESP and RESP models for non-polarizable FF |
| - Pre-defined and user-defined ESP and RESP models for polarizable FF |
| - Control of different charge constraints during the fitting steps |
| - Lone-pairs and extra-points |
| - United carbon atoms |
| - Correction of rounding-off errors of charges |
| - Statistics module for charges |
| * Atom typing |
| - AMBER and GLYCAM 2004 FF atom types for non-polarizable and polarizable FF |
| - User-defined atom typing |
| - Atom typing for molecules and molecular fragments |
| - Lone-pairs and extra-points |
| - United carbon atoms |
| * Building of FF libraries & FFTopDB |
| - The mol2 & mol3 file formats |
| - Format compatible with the non-polarizable and polarizable FF models |
| - Generation of large ensemble of FF libraries |
| - Whole molecules & molecular fragments |
| . Ligands & cofactors |
| . Amino-acid residues |
| . Nucleotide residues |
| . Monosaccharide & glycoconjugate residues |
| . Metal complexes |
| - Molecular fragment reconstruction & fusion |
| - Lone pairs and extra-points |
| - United carbon atoms |
| * FF parameter generation |
| - The frcmod file format |
| - AMBER and GLYCAM 2004 FF parameters for non-polarizable FF |
| - AMBER and GLYCAM 2004 FF parameters for polarizable FF (not available yet) |
| - Introduction of the q4md-forcefieldtools and of user-defined FF |
| - Lone-pairs and extra-points |
| - United carbon atoms |
| * Generation of a LEaP script |
| * MM energy value decomposition |
| - Energy decomposition for non-polarizable FF |
| - Energy decomposition for polarizable FF |
