Sort of different scripts written mainly in Python or Shell which are useful for QM/MM calculations using ChemShell, Turbomole and Amber.
Takes a list of atoms (like the ones from ChemShell scripts) and the complete pdb and generates a new pdb which includes only the atoms in the list.
Reads the status of calculations running in HPC servers and dumps it into a YAML Database.
Script for simplifying the analysis of NBO (by now) charges calculated using the dscf module from Turbomole, which can be obtained by adding the `$pop nba' keyword into the control file.
Takes an AMBER topology file and the coordinates (either inpcrd or pdb or mol2) and crops the water box removing all atoms outside a drop of a desired radius drawn around the selected residue. It also generates a list of atoms at a selected radius from an specified atom.
Takes the output of a QM/MM calculation from ChemShell (interfaced to either Turbomole or Gaussian) and plots the energies (QM/MM, QM and MM) along the optimisation of the structure or the optimisation of each point of a scan calculation
Takes the output of a hessian calculation of ChemShell (using the force module), parsers it and lets the user extract the most useful information such as the scructure of the QM zone (including the link atoms), a list of the calculated frequencies, the most contributing atom to a selected frequency and the contribution to a selected frequency of a selected atom.
Script from creating a multimodel/multiframe pdb file from a list of input files.
Script for printing a PES.plt file (generated with ChemShell for a PES exploration job) of a running job by inputting the job ID.
Parser for tags in LaTeX source files. It is able to read either a tex source file or a dict file (which is a plain text with a python dictionary in one line) and write an itemized line with the 'Table of Tags' chapter in a LaTeX source file or a dict file.
Script for creating a list of weights from a list of atoms. Four types of atoms can be considered. The output is a file containing a tcl list. Useful for some kind of jobs using ChemShell (like TS optimisations using the dimer method).
- Add example pics to description of each script which generates a plot.
- Add saving the pngs as an option (which can be modified modifing the script)