ALFchemY-MolPLACER

A basic code for creating a dimer from a molecule with accurate interplanar, x, and y displacements. If you find this code useful, please cite MolPLACER:

prerequisite:

• python3
• numpy

If not already installed, type "pip install numpy" in the linux terminal.

• MolPLACER 1.0 requires a planar fragment in your molecule. Please make sure that the first 3 atoms are in the reference plane. If the molecule is completely planar, it works perfectly.

Steps:

Steps to create a dimer with custom interplanar distance, x axis displacement and y axis displacement.
• Create an .xyz file of the molecule (monomer) in a directory.
• Rename the .xyz file to mol.xyz.
• Copy the two files (MolPLACER.sh,vect.py) of ALFchemY-MolPLACER to the same directory.
• Open a terminal in the directory and type "./MolPLACER".
• The code asks for the interplanar distance (in Angstrom) you desire for the dimer.
• Now, the code asks for one of the atom which is aligned to the x axis you disire.
• Enter the two atoms for defining the x axis one by one.
• Enter the x axis displacement
• Enter the y axis displacement
• You will find that a new file named "fixed.xyz" is created in the directory. Open it (Eg. in Mercury) and save it again in any other format (.mol2,.xyz,.pdb etc.) for further use.



Version 1.1.0

Now the code can rotate molecule along the z axis For a video tutorial, visit the following link: MolPlacer Tutorial

Please note that I am a beginner in coding and there are chances that the code can have some bugs.