tavolivos/Free-energy-landscape

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Created over 3 years ago
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tavolivos/Free-energy-landscape

tavolivos

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In this repository, we present a simple procedure to perform Free Energy landscape plots, taking results from molecular dynamics simulation.

Molecular-dyamics-protein-in-water

A tutorial to run molecular dynamics (protein in water) with Gromacs

Jupyter Notebook

Molecular-dynamics-Interaction-plot

Two scripts for MD interaction analysis (similar to interaction fraction on desmond).

Molecuar-Docking-with-Autodock4

A basic step-by-step tutorial to run molecular docking.

Jupyter Notebook

Download-multiple-sequencesfrom-NCBI-

This is a bash-script to download multiple sequences from NCBI with genus name.

Gromacs-GPU-installation

A bash script to install Gromacs (MP/GPU).

Download-Multiple-PDBs-from-Protein-Data-Bank

This is a bash-cript to download multiple PDBs from Protein Data Bank

Multiple-protein-protein-energies-interactions-with-Foldx

Multiple-protein-protein-energies-interactions-with-Foldx

Virtual-screening-semi-flexible-with-Autodock-vina

This is a bash script to analyse multipe ligands in a semiflexible receptor.

Molecular-dynamics-proteina-ligando

An step by step procedure to perform molecualr dynamics (protein-ligand complex) with gromcas (MPI GPU)

Jupyter Notebook

Distance-between-center-of-mass

This is a PyMol script to calculate distance between center of mass of two proteins from a set of selected residues.

The-Ligand-PATH

A TCL script to draw the ligand path along a molecular dynamics simulation.

Saving-GROMACS-trajectories-each-n-nanosecons

This script save GROMACS trajectories, independently, each "n" nanoseconds (e.g. each 1, 5, 10 ns, etc.). This is useful to avoid losses when files are damage for any kind of interruptions. It is also possible to restar the simulation from the last ns run.