This repository is to store some well-elaborated scripts to use in my everyday research life. Some of them may be interested to others.
This perl script is written by Marc Baaden to transfer GROMACS topology file or PDB file to psf file for other use
usage: top2psf.pl -p input.top [-P input.pdb] -o output.psf
I am working on transfering this perl script to python version to make compatible with my own script
This python script is to concatenate multiple psf files generated by top2psf.pl, with several options to include
usage: catpsf.py -p inputlist -w #ofsolventmol -o output.psf
This is a working python script that have similar function as Marc's perl script, top2psf.pl, to transfer GROMACS topology file to psf file for other use. (Right now we only support transferring atom and bond information to psf file)
usage: top2psf.py -p input.top -o output.psf
This python script is to build gaussian 16 input file from extracted PDB file, for both DFT and semi-empirical ZINDO calcualtions.
For protein ET, bridges are usually amino acid sidechains, we replace alpha-C with hydrogen to cap the sidechain as single molecule to include in QM calculations, and further specific feature is included in -s option
usage: geninp_g16.py -p input.pdb -n nprocshared -m memory -s specific_feature -o output
This python script is to build template gaussian 16 input file from extracted PDB file, in a clean and compact version comparing to previous
geninp_g16.py
usage: g16geninp.py -p input -n nprocshared -m memory -s specific_feature [-nt nterminal -ct cterminal] -o output
This python script is to calculate electronic coupling based on Block Diagonalization method.
usage: calHda_BD.py -f fock -s overlap -nb #ofbasis -ne #ofelectron -o output_prefix
This python script is to calculate electronic coupling based on orbital-based GMH method.
usage: calHda_GMH.py -f fock -s overlap [-m MO_coefficient] -d dipole [-no orbitals -al acceptor_list -dl donor_list -ml mo_list --length_threshold threshold]-o output