Always reload this page to be sure to read the latest version! PyRED version JUN 2023 - R.E.D. Server Development 2.0 Release of the sixth R.E.D. Server Development/PyRED version - 7-Zip is now used (instead of bzip2) to create archive files for PyRED jobs Dec 2024 (7-Zip outperforms traditional tools in terms of compression ratio) - Detect single/multiple molecule RESP fit failure and provide automatic assistance via email Dec 2024 (may occurs when large fits involving multiple molecules/conformations/orientations are ran) - Correct a warning/bug in PyRED related to moving QM files into the Mol_m'n' directories Nov 2024 (occurs when large numbers (> 9) of conformations and/or orientations are used) - Modify measurement units in JSmol/Jmol applets Nov 2024 - Modify the PyRED JOB1 output file if OPT_Calc = OFF1 to allow Jmol to read this file Nov 2024 - Compute 'equilibrium' values of dihedral angles (2 sorting approaches are proposed) Nov 2024 - Revisit the computation of equilibrium values of bonds and angles Nov 2024 (faster code, remove additional values and propose 2 sorting approaches) - Correct several bugs in the procedure, that allows requesting a private assistance (web site) Nov 2024 - Correct a bug in PyRED, that prevents the use of Re_Fit = ON and QM files from a previous job Nov 2024 (occurs if MP2 MEP output files from a previous job are used as input files for a new job) - Modify PyRED to reformat MM energy files and print atom types for all interactions Oct 2024 (see Mol_m'n'/Energy_m'n'-c'i'.txt files) - Recognize Gaussian output files to extract the optimized geometry, analyze the frequencies, Oct 2024 and compute accurate dE values between conformations (i. e. recognize Gaussian geometry optimization-frequency-single point energy output files) - Detect conformations with identical dE values involved in charge derivation, and Oct 2024 provide automatic assistance via email - A single QM output file can be uploaded without the need of creating an archive file Oct 2024 (Gaussian, GAMESS and Firefly/PC-GAMESS file formats are handled) - Analysis of QM versus RESP dipole moments is done for each optimized geometry/orientation Sep 2024 - Update the readme.txt, System.config and Project.config documentation Sep 2024 - Better handle total charge and spin multiplicity values in the different archive files Sep 2024 (Solve ambiguous cases if different values are reported in the Project.config, PDB input and QM geometry optimization output files) - Provide automatic assistance via emails to users if problems are detected during the Sep 2024 charge fitting step - Handle new atom types in Jmol/JSmol applets for accurate molecular visualization Aug 2024 - Provide automatic assistance via emails to users when certain keywords are misused Aug 2024 (List of handled keywords FRGAA/FRGNT, INTRA/INTER-MCC1/2, INTER-MEQA/B, OPT_Calc=OFF1) - Help users to determine the correct protation state(s) of the input molecules Aug 2024 (add new Jmol/JSmol commands if a failed geometry optimization is detected) - Correct a bug in the the PBS script when a failed frequency job is detected Aug 2024 (no Jmol/JSmol applet is generated) - R.E.D. Server Dev was attacked by a user using a web shell Jul 2024 (modify the codes of the web server and cluster to handle such an attack) - Correct a bug related to broken symmetry QM computation in the PBS script Jun 2024 - Correct a bug related to inter-molecular charge equivalencing during charge fit in PyRED Jun 2024 (rare case, when the RBRA approach is not used) - Correct wrong vocabulary in RESP input files in PyRED when Lagrange constraints are used May 2024 (use of intra/inter-molecular charge constraints and not restraints) - Update the documentation (readme.txt, System.config and Project.config files) May 2024 - Compute RMSE values from DIFF values (SM - IA/MM charge values) in the Stastistics files Apr 2024 (and replace DIFF values by absolute DIFF values) - Compute energy differences in kcal/mol and kJ/mol between molecular conformations Mar 2024 (carried out only if the number of conformations for a molecule > 1) - Update PyRED and the PBS script to display frequencies in new Jmol/JSmol applets Feb 2024 (carried out only if frequencies are computed or provided) - Correct a bug related to the computation of bond and angle equiibrium values Jan 2024 (this bug prevented the computation of the bond and angle values) - Compute equilibrium values for missing bond and angle force field parameters Dec 2023 - Development of informative popups for users from the php graphical interface Nov 2023 - Modify the format of the PyRED job graphical interface Nov 2023 (replace the html file format by the php one to allow developing more features) - Update the standalone graphical interface of PyRED jobs for R.E.D. Server Development Nov 2023 (make it compatible with PyRED at MatriCS https://www.matrics.u-picardie.fr/en/home/) - Update the home page of R.E.D. Server Development Oct 2023 (jmol applets are randomly loaded to provide various examples to users, among other modifications) - Bug correction related to the change of the user passsword Sep 2023 - Important bug corrections related to R.E.D. Server Dev. input submission procedures Sep 2023 (about the relation between RED Server Dev. and REDDB, about the size of the archive file, and about network connection problems between the web server and the cluster) - New set of checkings and corrections for the PDB input files and Project/System.config files Sep 2023 - Add a new section in the R.E.D. Server Development/PyRED tutorial Sep 2023 (section related to the creation of input molecules) - Update the q4md-fft builder Sep 2023 (add new commands related to the creation of missing hydrogen atoms and double/triple bonds) - Better handle wrong keywords in the Project.config/System.config files Sep 2023 (these wrong keywords are removed from the config files) - Add new features in PyRED for the Gaussian program after user requests Sep 2023 (new DFT functionals and new IOP for MEP computation are allowed) - Update the python version from 2.7.5 to 2.7.18 Sep 2023 - Revisit the display of different features in force field libraries using Jmol Aug 2023 (double and triple bonds, molecular dipole, molecular electrostatic potential) - Upgrade the php version of the web server Jul 2023 - Distances, angles, dihedral angles, hydrogen-bonds and five-membered ring pucker parameters Jun 2023 can now be computed using a new set of keywords provided in the Project.config file - Allow users to modify the font size and the background color of the html graphical interface Jun 2023 - Reinitialize the user database of the q4md-forcefieldtools.org web site (it is full) Jun 2023 (users, who need to use a private account will have to re-register) ----------------------------------------------------------------------------------------------------- PyRED version JAN 2019 - R.E.D. Server Development 2.0 Release of the fifth R.E.D. Server Development/PyRED version - Automatically handle the closure of RED Server Dev., when the user database is full May 2023 (users are warned, job submissions to REDServer Dev. are closed, and the user database is reinitialized after 21 days) - Bug corrections in Jmol/JSmol applets, when displaying mol2/mol3 files with gaff atom types Apr 2023 (chemical elements were not recognized, when gaff atom types were used) - Update in PyRED (script leaprc.q4mdfft) the documentation related to the LEaP program Apr 2023 (replace the html/missing amber6 documentation by a pdf version; the AmberTools12 manual) - Bug corrections in PyRED related to geometrical constraint used during geometry optimization Apr 2023 (atoms involved in a geometrical constraint were always sorted, which is not correct) - Update security issues in the REDServer Dev./PyRED tutorial and faq Mar 2023 - Update Jmol/JSmol applets related to mol2/mol3 files Mar 2023 (correct a bug related to atom radii, modify the display of the molecule, MEP, dipole) - Update the HTML interface Mar 2023 - Check and reformat the atom connectitivies provided by the user in the PDB input files Feb 2023 - Recompile the version 2.41 of the RESP program to handle up to 500 MEP for big jobs Jan 2023 (require large amount of RAM) - Modify the HTML interface to easely display the PDB/MOL2 files as text files in the browsers Jan 2023 - Better handle the PDB input file format with multiple conformations Dec 2022 - Provide help/information about the input/output files through the HTML interface Dec 2022 - Develop the HTML interface of each REDServer Dev.job, when killed by the admin/user/pbs Nov 2022 - Handle the PDB input file format with multiple conformations defined for RED perl Nov 2022 - Develop the q4md-fft builder to create PDB input molecules for REDServer Dev./PyRED Oct 2022 see http://q4md-forcefieldtools.org/REDServer-Development/Documentation/q4md-fft_builder.php - Major update of the REDServer Development/PyRED tutorial Oct 2022 see http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php - Release of the version 2.41 of the RESP program to handle a large number of molecules Sep 2022 (compilation with the -mcmodel=medium flag, increase qtol to 1.10-6, modify i4 vs i5 formats) - Increase the amount of RAM from 16 GB to 64 GB for 4 nodes (node10 to node13) Sep 2022 - Handling of the M062X DFT method by PyRED as requested by a user Sep 2022 - Update the readme.txt, System.config and Project.config documentation Aug 2022 - Update the tutorial http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php Aug 2022 - Rewriting/extending the emails sent to the users within the PBS script Jul 2022 (develop help to users, when error messages are generated by the QM programs) - Correct 2 bugs in PyRED related to QM computation with a pseudopotential Jul 2022 (in some cases wrong inputs were generated for the Gaussian program, which led to crashes) - Correct a bug in PyRED related to the computation of MEP when using the MP2 method Jul 2022 (increase the default SCF convergence criterion to allow MP2 computation using Gaussian) - Correct a php bug related to the 'Project name' definition during the input submission Jun 2022 (this bug prevented the registration of the Project in the REDServer dev. database) - Update the documentation (Project.config and System.config) Jun 2022 (try to better describe the INTRA/INTER-MCC1/2 and MOLECULE1-GEOMOPTCONST keywords) - Better recognize PDB input files with inappropriate formats within the PBS script Jun 2022 (improvement when multiple conformations are available in the PDB input files) - Correct a bug related to the display of the charge values in the Jmol/JSmol applets May 2022 (display of the sign of the partial charge values in the mol2/mol3 file formats) - Correct a PHP bug related to the simultaneous job submissions from different users May 2022 - Rewriting/extending the emails sent to the users within the PBS script May 2022 - Bug correction in PyRED related to the generation of optimized geometries to the PDB format Apr 2022 (occured when MEPCHR_Calc = OFF & the number of conformations > 1) - Handle hidden files (presence on Mac and Linux OS) within the PBS script Mar 2022 - Better handle wrong input filenames with special characters within the PBS script Mar 2022 - Set up of the "REMARK PROJECTCFG" and "REMARK SYSTEMCFG" keywords in the PDB input file(s) Fev 2022 (to bypass the use of the Project.config/System.config files in the archive file) See https://upjv.q4md-forcefieldtools.org/REDServer-Development/Documentation/readme.txt - Check for the presence of input files with the txt extension (& remove this extension) Fev 2022 (the file extensions may be hidden under the windows OS) - Modify the interface of the qstat command to help users to better follow their jobs Fev 2022 (extend the pieces of information printed in the temporary PyRED journal log file) - Handle the Gaussian "Optimization-Frequency" output file within the PBS script Fev 2022 (not originally recognized by PyRED) - Bug correction in PyRED related to the use of GAMESS Jan 2022 (definition of the scratch directory when a rst file is generated) - New PBS queueing script with many improvements to better handle the different input files Jan 2022 (with extensive explanations for the user) - Updated the readme.txt, System.config and Project.config documentation files Dec 2021 (Extend the description of the REDServer-Development/PyRED use & the reported keywords) - Slightly adapt the PDB input file format used by PyRED Nov 2021 (So that Jmol correctly displays the different conformations of a PDB input file) See https://upjv.q4md-forcefieldtools.org/REDServer-Development/Documentation/readme.txt - Modify Jmol & JSmol Applets to correctly handle AMBER atom types & MEP Nov 2021 (Check & display the chemical elements as well as multiple bonds/aromatic systems) - Identify the rare case, where two successive PBS jobs run in the same PXXXX directory Oct 2021 This appends because of a network problem (leads to corrupted data) - Updates of the Jmol (Java) & JSmol (js) applets generated by REDServer Dev. Sep 2021 - Reinitialization of the q4md-forcefieldtools.org user database Sep 2021 - Development of a new submission procedure for administrators useful for debugging Aug 2021 - Write a new JSmol applet to create new PDB input files for PyRED Aug 2021 (available from the doc & faq) - Better handle wrong PDB input filenames (special characters, double extension, etc...) Aug 2021 - Check for broken symbolic links and empty files within the archive file Aug 2021 - Better handle the permissions of the files within the archive file Dec 2020 - Implement the interface of Gaussian 16 C.01 Aug 2020 - Rewriting/extending the emails sent to the users Sep 2019 - Many Updates in the PBS queueing system script May 2019 - Use of SSL certificats for the web serveur and cluster Jun 2019 - Update the Qstat interface, and open the Ganglia monitoring system to users if needed May 2019 - Update of the documentation (overview, faq, config files) May 2019 - Increase the RAM amount of some nodes up to 64 GB Jun 2019 - Allows users to call powerful computational nodes Mar 2019 - Old Opteron based-computational nodes retired Jan 2019 - New virtual machine for the web server with an updated php version Jan 2019 - Protection of the frontal, NAS and storage servers with an inverter Jan 2019 - New storage server Jan 2019 - New frontal and NAS (home) servers for the cluster Jan 2019 - Use OPenPBSPro instead of Torque/Maui Jan 2019 - Upgrade to CentOS 7.6 the whole cluster Jan 2019 - Better handling of memory for Firefly and GAMESS May 2019 - Implement the interface of GAMESS Sept 2018 R3 May 2019 - Implement the interface of Firefly 8.2.0 Feb 2019 - New DFT models allowed after user requests Dec 2018 - Improvement of the Complex mode when using Gaussian Dec 2018 ----------------------------------------------------------------------------------------------------- PyRED version SEP 2015 - R.E.D. Server Development Release of the fourth R.E.D. Server Development/PyRED version - Modification of the strategy for generating force field parameters May 2016 (application to bioinorganic complexes) - Bug correction related to the control of the number of genereated fragments May 2016 - Introduction of new keywords to better handle the topology of the input molecules Sep. 2015 (particularly useful when generating a force field for a bioinorganic complex) - Introduction of a new keyword to control SCF convergence for MEP computation Sep. 2015 (particularly useful when generating a polarizable force field) - Introduction of a new keyword to control the number of generated molecular fragments Sep. 2015 (related to use of intra-molecular charge constraints) - Development of new models of lone-pairs for halogen atoms Sep. 2015 - Extension of the format of the frcmod.user input file recognized by PyRED Sep. 2015 - Bug corrections related to the geometry optimization procedure Sep. 2015 (to avoid recomputing jobs when input molecules are duplicated; leads to faster jobs) - Bug correction related to the STRIP mode when using Gaussian Sep. 2015 - Extension of the System.config documentation Sep. 2015 - Extension of the Project.config documentation Sep. 2015 - Update of the PBS script Sep. 2015 ----------------------------------------------------------------------------------------------------- PyRED version NOV 2014 - R.E.D. Server Development Release of the third R.E.D. Server Development/PyRED version - Bug correction related to the MOLECULE$n-CHEMEQxx keywords (xx = SM, IA and MM) Dec. 2014 - Bug correction related to the geometry optimization algorithm ('Normal' job) Dec. 2014 - Bug correction related to the Re_Fit mode (see filename modification in the 'Data-Default-Proj' directory) Dec. 2014 - Extension of the System.config documentation Nov. 2014 - Extension of the Project.config documentation Nov. 2014 - Extension of the readme.txt documentation Nov. 2014 - Update of the PBS script Nov. 2014 - New tutorials Nov. 2014 - The total charge value of a molecule can be defined in the PDB input file Nov. 2014 - Extension of the use of geometrical constraints during geometry optimization for GAMESS/Firefly (besides for Gaussian) Nov. 2014 - Extension of the use of various geometry optimization gradients for GAMESS/Firefly (besides for Gaussian) Nov. 2014 - Extension of DFT based charge models for GAMESS and Firefly Nov. 2014 - Modification of the frequency computation procedure, when using the 'Normal' mode Nov. 2014 (for GAMESS/Firefly and Gaussian) - Modification of the geometry optimization procedure of the 'Normal' mode (limit the number of steps, and re-run the job if convergence is not achieved) Nov. 2014 - New theory levels for geometry optimization and molecular electrostatic potential computation (implicit solvation in used defined options for Gaussian) Nov. 2014 - Release of new models of polarizable force field Nov. 2014 - Definition of user defined polarizability values in these two force field models Nov. 2014 - Interface of the resp 3.1 program (i.e. iresp from q4md-forcefieldtools) Nov. 2014 ----------------------------------------------------------------------------------------------------- PyRED version MAY 2014 - R.E.D. Server Development Release of the second R.E.D. Server Development/PyRED version - Extension of the archive recognition system May 2014 - Atom type CL vs Cl in the frcmod.user file used by the Demonstration service May 2014 - Extension 1 of the System.config documentation May 2014 - Extension 1 of the Project.config documentation May 2014 - Extension 2 of the Project.config documentation May 2014 - Add atom indexes in the Java applets May 2014 - New emails are automatically sent to the user to help understanding error messages May 2014 - Correct bugs in geometrical constraints during geometry optimization May 2014 - Complete the database of error messages when running a 'Complex' computation May 2014 - Update 1 of the readme.txt documentation May 2014 - Update 1 of the readme.txt documentation in the PyRED source code May 2014 - Modify Java applets to better display the atom labels May 2014 - Bug in the residue index in the mol2/mol3 file format corrected May 2014 - Recognition of the 7-zip archive format Jun. 2014 - Successive updates of the PBS script Jun. 2014 ----------------------------------------------------------------------------------------------------- PyRED version NOV 2013 - R.E.D. Server Development Release of the first R.E.D. Server Development/PyRED version Bug corrections and new features incorporated: New features - Extension of the HTML graphical interface generated by R.E.D. Server Development Jan. 2014 - Extension of the PBS script that executes each PyRED job Jan. 2014 - Re-define strange permissions of the input files provided in the Archive file Jan. 2014 - Extension of the Archive file recognition, and rewrite the corresponding documentation Jan. 2014 Bug corrections - Handle new file format found for Gaussian 09 D.01 Dec. 2013 - Gaussian output are not recognized when a Z-Matrix orientation is generated Feb. 2014 - INTRA-MCC with the 'Keep' flag are not correctly handled Feb. 2014 ----------------------------------------------------------------------------------------------------- Last update of this page: June 7th, 2023