News about the features implemented in
R.E.D. Server Development/PyRED


FF: force field

R.E.D. Server Development is open to all users.
See the documentation and Frequently Asked Questions.


 Features related to R.E.D. Server Development
    The linux Operating System used by R.E.D. Server Development is CentOS version 7.6 64 bits.

* Programs interfaced by R.E.D. Server Development
   - PyRED Jan. 2019
   - Gaussian 2016 ver. B.01 (64 bits binaries)
      (Binary provided by Gaussian Inc.; parallel computation with shared memory)
   - Gaussian 2009 ver. E.01 (same type of binaries as above)
   - Gaussian 2009 ver. D.01 (same type of binaries as above)
   - Gaussian 2009 ver. C.01 (same type of binaries as above)
   - Gaussian 2009 ver. A.02 (same type of binaries as above)
   - Gaussian 2003 ver. E.01 (same type of binaries as above)
   - GAMESS-US ver. Sept 2018 R3 (64 bits binary)
      (Binary compiled with Intel® 12.1 ifort & Intel® Math Kernel Library 12; parallel computation with sockets)
   - GAMESS-US ver. Sept 2018 R3 (64 bits binary)
      (Binary compiled with gfortran 4.8 & Intel® Math Kernel Library 12; parallel computation with sockets)
   - Firefly ver. 8.2.0 (32 bits binary)
      (Binary provided by the Firefly team; parallel computation with 32 bits OpenMPI 1.6 compiled with gcc 4.8)
   - Standalone version of the RESP program (version 2.4 or 3.1).

* Web interface to each PyRED job
   - Parse PyRED outputs
   - Jmol based graphical display (Javascript and Java versions).

* R.E.D. Server Development uses Apache (version 2.4.6) and Open PBS-Pro (version 18.1.3).


* Hardware: nodes
   - Two quad-cores Xeon E5430 processors (i. e. 8 cores) and 16 or 64 GB RAM used in each PyRED job, or
   - Two ten-cores Xeon E5-2690 v2 processors (i. e. 20 cores) and 256 GB RAM used in each PyRED job.

 Limitation in R.E.D. Server Development: 250 atoms

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
  - 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
  - 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

Any need or idea?   Please, contact us...                  


Last update of this web page: March 26th, 2019.

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