Generate meshes and pqr

Protein meshes and pqr

For the problems that involve proteins we use MSMS to generate the corresponding mesh. In order to achieve this we need to follow few steps:

  1. Download a pdb file from the Protein Data Bank http://www.rcsb.org/pdb/home/home.do

  2. Get the pqr file from the pdb.

  3. Install pdb2pqr from here: https://github.com/Electrostatics/apbs-pdb2pqr/releases or use the webserver: http://nbcr-222.ucsd.edu/pdb2pqr_2.1.1/

  4. Create pqr file. If you are running from command line:
    pdb2pqr --ff=amber input.pdb output.pqr

    where we picked amber as the force field.

  5. Create xyzr file:
    awk '{print $6,$7,$8,$10}' protein.pqr > protein.xyzr

    We are extracting certain columns from the protein.pqr we create in the previous step. We need the xyzr file as input for MSMS.

  6. Download MSMS from http://mgltools.scripps.edu/downloads.

  7. Create mesh from command line:

    ./msms_XX_XX/msms_XX_XX. -if protein.xyzr -of protein1 -prob 1.4 -d 2 -no_header

    If you want all the components, inside cavities you will add the flag

    -all_components

    Where _XX_XX correspond to the version you download. You can find information about the different flags here http://mgl.scripps.edu/people/sanner/html/msms_man.html

    If you want to add a Stern Layer you will need to create first the xyzr for Stern Layer and the generate the mesh. To do this:

    • Create the .stern file (i.e the xyzr for the stern layer) using the generateStern.py located in /pygbe/preprocessing_tools
    • Create mesh using MSMS setting -prob 0.5. For example:
    ./msms_XX_XX/msms_XX_XX. -if protein.stern -of protein1_stern -prob 0.5 -d 2 -no_header

Sphere and brick meshes

For problems that require spheres or bricks we generate the corresponding meshes by using the scripts mesh_sphere.py and mesh_brick.py. These scripts are located in /pygbe/preprocessing_tools.