This directory contains the various scripts needed that are not available online and this README file contains some more information on usage, license, etc.

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Tere are 2 modified version of the Plumed partial_tempering script:

1) partial_tempering_only_torsions.sh
	Only changes the torsions of the given topology file

2) partial_tempering_only_torsions_and_zeroed_NB_interactions.sh
	Changes the torsions of the given topology file and sets the LJ and Q interactions to zero

For usage instructions execute the script with the --help flag:
$ ./partial_tempering_only_torsions.sh --help

The scripts are open source software covered by the same license as Plumed: LGPL-3.0 license (a copy of it is given in the etc/ directory)

More information about the Plumed software can be found here https://www.plumed.org/

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Tere are some python scripts to more easily use the partial tempering scripts in the way we used them:

1) create_only_torsions_top_complex.py
	The structure and topology files must be called complex_with_dummy.gro complex_with_dummy.top and the ligand resname must be LIG
	It will scale the dihedrals of the ligand and first neighbors, creating 16 topology files with the 0 topology being unchanged and the most scaled one having the dihedral costants scaled by 0.2 (new = old * 0.2)

2) create_only_torsions_top_ligand.py
	The topology file must be called LIG.top
	It will scale the dihedrals of the ligand and first neighbors, creating 16 topology files with the 0 topology being unchanged and the most scaled one having the dihedral costants scaled by 0.1 (new = old * 0.1).
	It can be used to do the HREM of the ligand in water or ligand in vacuum if you don't want to set the NB interactions to zero (we used it for the ligand in water).

3) create_zeroed_top_ligand.py
	The topology file must be called only_LIG.top
        It will scale the dihedrals of the ligand and first neighbors, creating 16 topology files with the 0 topology being unchanged and the most scaled one having the dihedral costants scaled by 0.1 (new = old * 0.1).
	And it will set the NB interactions to zero (Q and VdW interactions).
        It can be used to do the HREM of the ligand in vacuum, when afterwards you use couple-intramol=yes to generate it in a box of water like we did.

To use them you need a python environment equivalent to the one needed to use HPC_Drug https://github.com/MauriceKarrenbrock/HPC_Drug (see the environment.yml file on the github page).

Usage:
$ python $SCRIPTNAME

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There is the reorder_atoms.py that reorders the atoms of a PDB file according to a reference, it was used to reorder the atoms after docking with autodock as it does not keep the original order
The filenames must be reference.pdb and input.pdb, a file called output.pdb will be generated
Warning: the PDB files must only contain the ATOM and/or HETATM lines, nothing more (no check is done)

The script is open source software covered by the GNU GPL-2.0 license (a copy of it is given in the etc/ directory)

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There is the make_tpr_LT.py script that generates the script to make the starting TPR files for the Loose-Tight restaint

$ python make_tpr_LT.py

Edit the two variable names: "kind_of_ne" "name_of_mdp_file_without_suffix" get the wanted behaviour

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All software where the license has not been specified is covered by the MIT open source license (a copy of it is given in the etc/ directory)

