#Primordia wiki how to#
#Primordia wiki pdf#
#Primordia wiki install#
#Primordia wiki download#

Journal of Chemical Information and Modeling, 60(2), 578-591. Elucidating Enzymatic Catalysis Using Fast Quantum Chemical Descriptors. Journal of Computational Chemistry, 41(9), 862-873. Semiempirical methods do Fukui functions: Unlocking a modeling framework for biosystems. This tutoral uses the Google Colab cloud computing plataform and thus you can run from any operational system machine: We also provide an specific tutorial to run PRIMoRDiA without needing to configure your local machine.

#Primordia wiki pdf#

We provide full tutorials in a PDF file of all calculations modes of the software, as pratical applications for acid force and enzymatic catalysis reaction.

#Primordia wiki how to#

We provide a complete description of the descriptors and how to use the program in a user guide pdf file.Īll the theory basis, references and how to prepare the quantum chemistry calculations are detailed in these files. The detailed instructions of these two intallation options are described in our wiki home.

#Primordia wiki install#

We strongly recommend the latter to maximize the performance of the software in your machine.įirst install Eigen3 library and the g++-8.

#Primordia wiki download#

You can download the executable file or just compule the software usinf CMAKE. Adjustments in visualization scripts and statistical analysis.Volumetric and Condensed representation for all local descriptors.New calculations methods for local hardness.Important adjustments in scripts for Pymol grpahical visualization.Implementation of the global and local composite hardness.Molecular Dynamics trajectory automatic calculation and generation of scripts for statistical analysis.Reaction path trajectory automatic calculation and generation of scripts for statistical analysis.

New input format, more intuitive and complete for the new analysis.

In the next versions this feature will be included along with the support for other quantum chemical packages PRIMoRDiA 1.2v - Important Stable UpdateĬurrently, this version is under tests and will be released soon and will include all features of the 1.0v along with important updates listed below.

PRIMoRDiA 1.1v - Unstable Internal Versionįeatures related with TERACHEM support via molden files. Make R scripts to automate Density of States (DOS) plot.Outputs those reactivity descriptors either in Cube files or in numerical values assigned to each atom.Implements local reactivity descriptor methods adjusted for macromolecules.Caluclate Local Reactivity Descriptors for residues from biological systems ( set in PDB files, such as protein adn DNA fragments ).(Four working methods for Local hardness, Local Softness, hyper softness, local electrophilicity, multiphilcity, Fukui functions, electron density, and other common local electrostatic properties) (Hardness, softness, Ionization Potential, Electron Affinity, and more six related with electronic energies) Calculates Global reactivity descriptors.Installation instructions and tutorials are in our wikiĪll theoretical background and working instructions of our program are in our userguide pdf file that can be found in this repository. Structure of the molecules, as also other electrostatics properties. The main reactivity descriptors of the Conceptual Densityįunctional Theory, the most famous and used reactivity theory, which works from response variables of the electronic It to generate several descriptors to calculate the global and Written in C++ for post electronic structure calculations, thatĮfficiently reads output files from most used quantum mechanics packages, storing molecular information and processing PRIMoRDiA ( PRIMoRDiA Macromolecular Reactivityĭescriptors Access ) is a shared memory parallel software