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pKa prediction using PDB2PKA (EXPERIMENTAL)

Contents

  1. 1 Introduction
  2. 2 Installation
    1. 2.1 APBS Installation
    2. 2.2 PDB2PQR Installation
  3. 3 Running PDB2PKA

Introduction

Starting from PDB2PQR-1.5 there is an experimental pKa prediction tool called PDB2PKA, which is based on both PDB2PQR (for adding limited missing atoms, H-bond optimization, etc.) and APBS (for PB-based energy calculations).  The instructions for running PDB2PKA are as follows:

Installation

APBS Installation

  1. APBS must be 1.2 or later versions.
  2. configure with the --enable-python option, e.g.,  
    $ ./configure --prefix=/tmp/apbs_inst_dir --enable-python
  3. $ make; make install

PDB2PQR Installation

  1. PDB2PQR must be 1.5 or later versions.
  2. configure with the --with-apbs option, e.g.,  
    $ ./configure --with-apbs=/tmp/apbs_inst_dir/bin/apbs
  3. $ make; make install

Running PDB2PKA

From pdb2pqr/pdb2pka/ directory, run

$ ./pka.py [options] mypdb.pdb

which should get PDB2PKA started.  When PDB2PKA is finished, the result file name should look like mypdb.pdb.PKA.DAT.  The completion time is dependent on size of the pdb file, system configuration, etc.

Options for PDB2PKA include the following:
  • -h, --help:    display usage information and exit.
  • -v, --verbose:    print information to stdout.
  • --pdie=PDIE:    protein dielectric constant, default value is 8.
  • --sdie=SDIE:    solvent dielectric constant, default value is 80.
  • --ff=FF:    force field used in PDB2PKA, the default force field is PARSE, currently there is no support for other force fields due to lack of parameters for neutral N-terminal and neutral C-terminal residues.
  • --ligand=LIGAND:    ligand in mol2 format.
  • --maps=MAPS:    1 for using provided 3D maps; 2 for genereting new maps.
  • --xdiel=XDIEL:    xdiel maps
  • --ydiel=YDIEL:    ydiel maps
  • --zdiel=ZDIEL:    zdiel maps
  • --kappa=KAPPA:    ion-accessibility map
  • --smooth=SD:    st.dev [A] of Gaussian smooting of 3D maps at the boundary, bandthwith=3 st.dev
  • --res_energy=DESOLVATION_RES:    Calculate desolvation energy and interaction energy for this residue in its default protonation state.  Protonation states can be specified with the --protonation_state argument
  • --PS_file=PS_FILE:    Set protonation states according to the pdb2pka protonation state file (option --PS_file)


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