Simple scripts for automating some steps of Justin A. Lemkul's tutorial for Gromacs. Useful mainly for simulations with large series of ligands.

-> Topology Ligands

*Fix.py

• Searches for '.mol2' files and run the script 'sort_mol2_bonds.pl' generating the '_fix.mol2'.

      python3 fix.py 
  

*pos_cgenff.py

• Use after generating '.str' on CGenff site - Script searches for '_fix.mol2' and '.str' runs the 'cgenff_charmm2gmx_py3.py' script to generate the '_ini.pdb' used in the sequence by 'editconf' to generate '.gro'

      python3 pos_cgenff.py
  

-> Topology Complex

*complex.py and complex_lig_cof

• The script create complex.gro file it is merge prot.gro with lig.gro (or lig and cof) keeps the box_vector of prot and changes the total number of molecules at the beginning of the file.

      python3 complex.py prot.gro lig.gro
  
      python3 complex.py prot.gro lig.gro cof.gro
  

*topol_lig.py and topol_lig_cof.py

• Depending on topol_ it includes in topol.top file: ligand parameters, ligand topology and molecules at the end of the file.

      python3 topol_lig.py lig 
  
      python3 topol_lig_cof.py lig cof
      (do not put extension)
  

*topol_POSRES_lig.py and tpol_POSRES_lig_cof.py

• Restraining the Ligand Step - Include the position restraint topology information in our topology file.

• Restrain only ligand whenever but if you want a bit more control during equilibration, i.e. restraining the protein and ligand independently, change #ifdef POSRES to #ifdef POSRES_LIG in script file

      python3 topol_POSRES_lig.py
      
      python3 topol_POSRES_lig_cof.py
  

*remove_SOL.py

• For gas-phase simulations, input solv_ions.gro and the script remove SOL from the file, change the final number of molecules and return prot_ions.gro.

      python3 remove_SOL.py
  

*lig_preparation_gmx.py

• The three steps above in only one.

• Automates the preparation of ligand. Download script sort_mol2_bonds.pl and cgenff_charmm2gmx.py for use this.

• Putting the script in the directory with ligands in .mol2.

• It perform the script sort_mol2_bonds.pl obtain fix.mol2 obtain the .str file from CGenFF website runs the script cgenff_charmm2gmx and generates the .gro file by editconf.

• Finally creates directories for the results of each ligand.

      python3 lig_preparation_gmx.py
  

*complex_topol.py

• This script must be run in the directory under analysis. It creates the complex.gro file and makes adjustments to topol.top. Used for protein and ligand or protein ligand and cofactor.

• Extensions MUST be added.

      python3 complex.py prot_name lig_name cof_name
  

*analises_gmx.py

• Obtains only the "center" and/or "fit" trajectory for solvent or gas-phase complexes (pcouple = no, only nvt equilibrium) with sv_trj and gp_trj or sv_all = RMSD, RMSF, SASA, Gyrate.

• Changing the name of the .tpr in "cmd"

      python3 analises_gmx.py <sv_all or sv_trj or gp_trj>