Program for revealing non-covalent interactions
License
juliacontrerasgarcia/NCIPLOT-4.2
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Folders and files
Name | Name | Last commit message | Last commit date | |
---|---|---|---|---|
Repository files navigation
NCIPLOT is a program for revealing non covalent interactions based on the reduced density gradient. Please cite: * NCIPLOT-4.0: DOI: https://pubs.acs.org/doi/10.1021/acs.jctc.0c00063 For more information and updates, visit our webpage: http://www.lct.jussieu.fr/pagesperso/contrera/index-nci.html Developer of the 4.0 version: Roberto A. Boto * Overview NCIPLOT is a program that enables graphical visualization of inter and intramolecular non-covalent interactions (i.e. hydrogen bonds, steric clashes and van der Waals) in systems ranging from small molecules to large biosystems. NCI (Non-Covalent Interactions) is a visualization index based on the electron density and its derivatives. It enables identification of non-covalent interactions, based on the peaks that appear in the reduced density gradient (RDG) at low densities. RDG isosurfaces for these peaks enable the visualization of weak interactions. The isosurfaces correspond to both favorable and unfavorable interactions, as differentiated by the sign of the second density Hessian eigenvalue. The sign of this eigenvalue, times the density, is able to characterize both the strength and (un)favourable nature of the interactions and defines the isosurface colouring. See the reference below for a thorough explanation of the details. This program reads a gaussian-style wfn or wfx file or a geometry xyz file and computes density and reduced density gradient (RDG) on a grid. It can provide cube-format cube files and VMD scripts for the direct visualization of the results. * Compilation To install nciplot, unpack or clone the contents of the distribution and cd into the src_nciplot_4.0/ subdirectory. Change the Makefile.inc to suit your compiler and flags, and do: make mrproper make to build the nciplot executable. To clean the object and module files, make clean To clean objects, modules and binaries, make mrproper NCIplot requires the NCIPLOT_HOME environment variable to find the atomic density files contained in the dat/ subdirectory. Set it to the absolute path to NCIplot: export NCIPLOT_HOME=/home/xxxx/nciplot/ You may add the previous line to your .bashrc or .bash_aliases file for convenience. The code has been parallelized for shared-memory architectures using the OpenMP library. To use this feature, set the OMP_NUM_THREADS environment variable to the number of cores: export OMP_NUM_THREADS=4 Several tests and examples are provided in the tests/ directory. The PDF manual is simply NCIPLOT_MANUAL.pdf which is shipped with the code. Only the usage of the code suggested in the manual is recommended. As a brief outline, the accepted keywords in this version are: !===============================================================================! ! Read optional keywords. ! Accepted keywords in this version: ! - RTHRES ! - LIGAND ! - RADIUS ! - INTERMOLECULAR ! - ONAME ! - INCREMENTS ! - OUTPUT ! - FRAGMENT ! - CUTOFFS ! - CUTPLOT ! - ISORDG ! - INTERCUT ! - DGRID ! - RANGE ! - CG2FG ! - INTEGRATE ! - FINE ! - ULTRAFINE ! - COARSE !===============================================================================! Have fun!
About
Program for revealing non-covalent interactions
Resources
License
Stars
Watchers
Forks
Releases
No releases published
Packages 0
No packages published