mpsica / cd28_apbs_tool

Tools to calculate Difference between APBS maps

CD28_APBS_tool

Tool to calculate Difference between APBS maps

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Soft requirements:

• Bash

• R (Special libraries: none)

• APBS (1), available in: https://github.com/Electrostatics/apbs. In Linux (Ubuntu) APBS can be installed from repositories. Type in terminal:

    sudo apt install apbs
  

• PDB2PQR, available in: https://pdb2pqr.readthedocs.io/en/latest/getting.html

(1) Adaptive Poisson-Boltzmann Solver are calculated using the apbs tool developed in: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001.

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We provide two scripts: Delta_q_script.sh and _func.R. With these scripts we calculated the difference between to maps generated by APBS. APBS requieres the structure to be formated as PQR. PDB2PQR is the tool for this conversion. Delta_q_script.sh is a wrapper script that performs these two steps and then parse the maps to _func.R to perform the final calculation.

To begin, using the same imput PDB structure, the script first calcultes two APBS maps at two different pH values (5 and 7, but Delta_q_script.sh can be edited to change any of these values). The maps produced by APBS (.dx files) are 3D matrices, so to calculate the difference between maps a simple script in R (_func.R) calcultes an element-wise subtraction. For that reason it is important that APBS maps at both pHs are calculated over the same input structure. The substracton is calculated as map_at_pH7 minus map_at_pH5 so positive difference (Delta_q > 0) means an increase in positive charge (or decrease in negative charge).

Remember to give execution permission to these scripts.

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Instructions:

1. Load the pdb structures in the current working directory (CD28.pdb is provided with this repo) together with Delta_q_script.sh and _func.R.

2. Run the script as ([protein]=CD28 in our case):

    ./Delta_q_script.sh [protein].pdb
   

3. The output file (Delta_q-[protein].dx) will be created in the same directory.

4. To observe the maps in 3D around the protein in Pymol (as in Fig. 6A&B), the Delta_q-[protein].dx can be loaded together with the input PDB file. Also VMD or Chimera can be used.