Table of Contents
Molecular modelling lab Wiki
Saving time howtos
PyMOL
AutoDock
AMBER howtos
GAUSSIAN howtos
COOT & Phenix
cMM-ISMSA
Images
Molecular modelling lab Wiki
Saving time howtos
N-times commands
Remove unwanted lines from a file, e.g. ANISOU records in a PDB file
Copy files/directories across machines preserving mode, ownership and timestamps
PyMOL
Movies
Renumber residues / Rename chains, residues or atoms
Magic commands
Get atom IDs for QM/MM from PyMOL
Merging PyMOL sessions
Draw a cartoon from CA-coordinates only
AutoDock
how to proceed
some hints
AMBER howtos
Concatenate trajectories
Remove/Keep (specified) waters and ions
Run 3-steps minimization
Run Molecular dynamics simulation from minimized structure
Calculate RMSD of elements of the simulation
QM/MM setup for reaction coordinate
QM/MM setup for reaction coordinate calling Gaussian as an external program
QM/MM setup for reaction coordinate (Amber16)
2D Umbrella sampling executable
Heating ramp with restart
Minimization, heating and equilibration using GPU
Clustering using ptraj
Superimposing residues from a trajectory using cpptraj
PDB generation from different RST files using cpptraj
GAUSSIAN howtos
Geometry optimization and Molecular Orbital (MO) calculations
AMBER PREP file preparation
Visualizing Gaussian output files using Molden
COOT & Phenix
example of a parameter file containing LINK info for PDB entry 2WOW
cMM-ISMSA
Installation
Analysis of multiple trajectories and generation of a CSV file with R
Images
PNGs to GIFs - Ana Negri's way