EPB Charge: This is a set of tools for the calculation of polarized ligand charge from a protein-ligand complex structure with the EPB method.

EPB - Effective Polarizable Bond

Author: GuanFu Duan, [email protected]

Supervisor: Changge Ji

All rights reversed 2019    

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Installation

Follow these steps on Linux/OSX:

• Download and install Python (Version > 2.7)

  Example: Download the lastest 64-bit Ubuntu/Linux Python 3 file Miniconda3-latest-Linux-x86_64.sh and run

                chmod +x Miniconda3-latest-Linux-x86_64.sh
  
                ./Miniconda3-latest-Linux-x86_64.sh
  

• Dependency Package(openbabel、pybel、openmm and pdbfier) and Program EPB-master installation

  Download the EPB-master.zip and decompression it

  • Install dependency package

    

    • OpenMM: A High Performance Molecular Dynamics Library (Related paper)

    • OpenBabel: An open chemical toolbox (Related paper)

            conda install -c omnia openmm pdbfixer
      
            conda install -c openbabel openbabel
      
            pip install pybel
      

  • Install Program EPB-master in two methods:

    • Method I:

            cd EPB-master
      
                chmod +x EPBLigCharge.py
      

      • using "./EPBLigCharge.py -h/--help" for help

    • Method II:

            cd EPB-master/package
      
                chmod +x INSTALL.py ./bin/EPBLigCharge.py  
      
                ./INSTALL.py  
      
                source ~/.bashrc    
      

      • using "EPBLigCharge.py -h/--help" for help

Sugguest using second method to install Program EPB-master

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Instructions

Open the terminal in Mac/Linux and run "EPBLigCharge.py -h/--help"

usage: EPBLigCharge.py [-h] [-p PROTEIN_FILENAME] [-l LIGAND_FILENAME]
                   [-c {eem,eem2015ba,eem2015bm,eem2015bn,eem2015ha,eem2015hm,eem2015hn,eqeq,fromfile,gasteiger,mmff94...}]
                   [-u {0,1}] [-o OUT_LIG_NAME] [-f {mol2,pdb,None}]
                   [-n TEMP_NAME] [-t {0,1}] [-k {0,1}]

A tool: calculation of polarized ligand charge from a protein-ligand complex structure with the EPB method.

optional arguments:
    -h, --help            show this help message and exit
    -p PROTEIN_FILENAME   Read the pdbid or receptor file(pdb).
    -l LIGAND_FILENAME    Read the ligand file(pdb/mol2).
    -c {eem,eem2015ba,eem2015bm,eem2015bn,eem2015ha,eem2015hm,eem2015hn,eqeq,fromfile,gasteiger,mmff94,none,qeq,qtpie}
                          the charge model using in pybel format convert (default: mmff94).
    -u {0,1}              When input is a mol2 file for ligand, use the current charge, 0)No(default), 1)Yes.
    -o OUT_LIG_NAME       Define the output filename(deafult name: LigWithNewCharges).
    -f {mol2,pdb,None}    Output format: mol2(default), pdb, None(represents output mol2 and pdb file at the same time.)
    -n TEMP_NAME          Define the temporary folder name (default: tmp_file) which store the temptorary file(default:
                          tmp_file.dat).
    -t {0,1}              whether reserve the temporary file and store in temporary directory. 0)NoSave(default), 1)Save.
    -k {0,1}              Whether draw the ligand picture, 0)No(default), 1)Yes.

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Examples

• Calculate polarized ligand charge from a complex structure which from https://www.rcsb.org/

  • Example of how to run the code:

              EPBLigCharge.py -p 1g5s -t 1
    

  • The output:

    • 1g5s.pdb (suppose 1g5s.pdb not in current directory, it will download from https://www.rcsb.org/)

    • LigWithNewCharges.mol2 (the ligand file with polarized charge calculated by EPB)

    • tmp_file (is a folder, and contain some temporary files, the information is written in tmp_file.dat)

• Calculate polarized ligand charge from a complex structure which from local

  • Example of how to run the code:

              EPBLigCharge.py -p ./example/1g5s.pdb -t 1
    

  • The output:

    • LigWithNewCharges.mol2 (the ligand file with polarized charge calculated by EPB)

    • tmp_file (is a folder, and contain some temporary files, the information is written in tmp_file.dat)

• Calculate polarized ligand charge from a ligand file and a receptor file

  • Example of how to run the code and the ligand format is "pdb":

              EPBLigCharge.py -p ./example/1g5s_receptor.pdb -l ./example/1g5s_ligand.pdb -t 1
    

  • Example of how to run the code and the ligand format is "mol2":

              EPBLigCharge.py -p ./example/1g5s_receptor.pdb -l ./example/1g5s_ligand.mol2 -t 1
    

  • The output:

    • LigWithNewCharges.mol2 (the ligand file with polarized charge calculated by EPB)

    • tmp_file (is a folder, and contain some temporary files, the information is written in tmp_file.dat)

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