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protocolGromacs

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Automatic gromacs protocol from preparation to production with ligand parametrization through

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# Automatic Gromacs Workflow Script
*Author: Thibault Tubiana, PhD*  
**Please read before using this script.**

## Description
This script is made to facilitate the preparation and production of protein and protein/ligand, MD.  
It follows the procedure described for teaching I made at the University of Bergen. You can find lectures content on this page http://tubiana.me/teaching/kjem220-molecular-modelling/ or the pdf describing all the steps on this script here: http://tubiana.me/teaching_files/biocat2020/Tutorial_Gromacs-2019.pdf 
Fundamental analysis is also generated with gromacs tools (temperature/pressure/rmsd/rmsf/...), and the production trajectories are also cleaned with trjconv (imaging/protein centred/water stripped), but all the original trajectories are kept.  
Feel free to make other analysis of course, like trajectory clustering with TTClust https://github.com/tubiana/TTClust 😇

## Disclamer
* Each system is unique. This protocol and MD parameters is not adapted for all systems. If your system crash, you may have to tweak MDP parameters.  
* Ligand parametrisation is *"quick and dirty"*, For a more stable MD system you may have to tweak ACPYPE parameters (and check the hydrogens that are added with babel).

## Dependencies
- this script only works on Linux (maybe Mac) and use the BASH syntax.
- For ligand parametrisation, I use ACPYPE (https://github.com/alanwilter/acpype) which can generate parameters for Amber, Gromacs and Charmm. Please cite this paper if you use ACPYPE: https://doi.org/10.1016/j.softx.2019.100241.  
   1. To install ACPYPE, I sugg0est you to install first Miniconda (if you don't already have conda https://docs.conda.io/en/latest/miniconda.html) and the create a new conda environment with the command `conda create -n acpype -c conda-forge acpype` 
   2. then activate the environment with `conda activate acpype`
   3. Hydrogens on ligand: openbabel. You can install it with `conda install -c conda-forge openbabel`
   
Here's a unique command line to create a environment with every depencencies  
`conda create -n gmx -c conda-forge -c salilab acpype dssp`  
you can activate the environment with `conda activate gmx`

## How to
1. Make sure you have all the dependencies 
    1. If you have a protein-ligand system, make sure acpype is installed (see **parameters**)
    2. Gromacs
    3. (optional) DSSP version 3
2. Clone this repository with the command `git clone https://github.com/tubiana/protocolGromacs.git`
3. Put your PDB in the repository
4. Make the change you need in runGromacs.sh (See **parameters**)
5. run the script with `bash runGromacs.sh`

## Parameters
You have to make some changes in the script file (runGromacs).
- **FILE**: PDB filename **without the extension** (2h4g.pdb --> FILE=2h4g)
- **LIGNAME**: 3 letter ligand name (it has to be the same in the PDB). NOTE: **The ligand name will be change to `LIG` afterward.**
- **BOXSIZE**: Periodic box size in nm (between protein and box facet) default is **1.2**
- **BOXTYPE**: Box type. Default is **cubic** (see http://manual.gromacs.org/documentation/5.1.4/onlinehelp/gmx-editconf.html for more details)
- **NT**: Number of CPU cores. Default is **8**
- **WATER**: Water-type. Default is **tip3p**
- **NUMBEROFREPLICAS**: Number of replicas (the same simulation will be done 3 times from the minimisation). Default is **3**
- **FF**: Force field, default is **amber99sb-ildn**
- **SIMULATIONTIME**: Simulation time in `ns`. Default is **100**. The script will automatically calculate and modify the number of steep according to the timestep in mdp/md_prod.mpd.

## Workflow

Here's a picture describing the workflow in this script, but you can find more information on each step on my tutorial http://tubiana.me/teaching_files/biocat2020/Tutorial_Gromacs-2019.pdf. You can, of course, modify my script as you want :-)

![](https://raw.githubusercontent.com/tubiana/protocolGromacs/master/img/gromacs_protocol.png "gromacs_protocol")

## folder structure
Here's a description of the folder structure after a simulation job:
```
|-- .                             #--> repo folder, the script, the initial structure and topologie files
    |-- param                     #--> only if ligand is present, will contain receptor and ligand parameters
        |-- receptor              #--> receptor structure and topology
        |-- ligand                #--> receptor topology
            |-- ligand.acpype     #--> ligand topology
    |-- mdp                       #--> original mdp parameters
    |-- replica_X                 #--> simulation for replica number X (if 3 replica, then 3 folders)
        |-- graph                 #--> All the output graph are saved here (rmsd,rmsf,energy.....)
        |-- gro                   #--> Some output structures from MD are saved here
        |-- mdp                   #--> copy of previous mdp folder
        |-- results               #--> contains the MD
            |-- mini              #--> minimisation MD files
            |-- nvt               #--> heationg MD files
            |-- npt               #--> equilibration MD files
            |-- prod              #--> production MD files
```

## Last thing...
Have fun with MD and send me a mail if or open an issue if you have any problems, or just if you used this script and want to thanks me, I will be please to know that it was useful for someone 🙂

Thibault Tubiana.

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