How to perform APBS calculations
(please see click for Yang lab website)
Contents
Getting a PDB file of your own model system
Pick your favorite model system. This can be one snapshot from your own simulation trajectory or downloaded the protein databank.
Here, we plan to use a simple protein-DNA complex, estrogen receptor bound to DNA.
The PDB code is 1HCQ
Introduction to electrostatic calculations with APBS: using the PDB2PQR/APBS web services
The website name has been changed several times. Here is the current web-link,
http://nbcr-222.ucsd.edu/pdb2pqr_2.1.1/
It is easy to use because the authors did a wonderful job in making it user-friendly.
Now, we will go through the process in class. It is quite straightforward if you follow the instructions (with default parameters unless specified.
The APBS calculation will take a couple of minutes to finish and then you’ll be shown the results page.
Outputs of APBS calculations
Three major files are generated. They look like:
14556524059.pqr apbsinput.in 14556524059-pot-PE0.dx.gz
The first two files are two input files required for APBS calculations: a PQR file and an input file describing the APBS calculation.
Now you can download them into your local machine/laptop
Right click to download
An example of the input file:
read mol pqr 14556524059.pqr end elec mg-auto dime 161 97 257 cglen 110.345 57.0452 193.912 fglen 84.909 53.556 134.066 cgcent mol 1 fgcent mol 1 mol 1 lpbe bcfl sdh pdie 2 sdie 78.54 srfm smol chgm spl2 sdens 10 srad 1.4 swin 0.3 temp 298.15 calcenergy total calcforce no write pot dx 14556524059-pot end quit
Some details about the input file is discussed in the APBS wiki.
An example of a pqr file:
REMARK 1 PQR file generated by PDB2PQR (Version 2.0.0) REMARK 1 REMARK 1 Command line used to generate this file: REMARK 1 --with-ph=7.0 --ph-calc-method=propka --apbs-input --ff=parse --verbose --summary 1hcq 1hcq.pqr REMARK 1 REMARK 1 Forcefield Used: PARSE ... REMARK 6 Total charge on this protein: 10.0000 e REMARK 6 ATOM 1 N MET 1 50.465 24.781 79.460 -0.3200 2.0000 ATOM 2 CA MET 1 50.332 26.116 80.055 0.3300 2.0000 ATOM 3 C MET 1 49.978 25.999 81.550 0.5500 1.7000 ATOM 4 O MET 1 50.739 26.439 82.436 -0.5500 1.4000 ATOM 5 CB MET 1 49.385 26.972 79.200 0.0000 2.0000 ATOM 6 CG MET 1 49.572 26.667 77.705 0.2650 2.0000 ATOM 7 SD MET 1 48.684 25.175 77.141 -0.5300 1.8500 ATOM 8 CE MET 1 47.010 25.835 76.891 0.2650 2.0000 ATOM 9 HE1 MET 1 46.439 25.570 77.664 0.0000 0.0000 ATOM 10 HE2 MET 1 47.061 26.829 76.828 0.0000 0.0000 ATOM 11 HE3 MET 1 46.637 25.458 76.047 0.0000 0.0000 ATOM 12 H2 MET 1 50.024 24.770 78.561 0.3300 0.0000 ATOM 13 H3 MET 1 51.435 24.556 79.358 0.3300 0.0000 ATOM 14 HG2 MET 1 49.269 27.489 77.169 0.0000 0.0000 ATOM 15 HG3 MET 1 50.578 26.578 77.518 0.0000 0.0000 ATOM 16 H MET 1 50.027 24.105 80.054 0.3300 0.0000 ATOM 17 HA MET 1 51.216 26.580 79.986 0.0000 0.0000 ......
The last two columns are charge and radius, respectively.
Visualization of electrostatic potentials using VMD
Maps of electrostatic potentials around biomolecules are useful in determining possible interaction sites for protein-protein and protein-DNA interactions. Electrostatic potentials can be obtained by solving the Poisson equation for a given molecular structure.
Here, we we will use VMD in order to visualize the APBS-calculated electrostatic potentials.
a. Download VMD if needed. b. Load *.pqr into vmd c. Click “File” --> Load data into Molecule and pick *.dx file d. Go to “Graphics” --> Representation and click Rep button e. Go to “Dray style” tab of the graphical representations window and change Drawing Method to “Surf” (or "isosurface") and Coloring Method to “Volume” f. Go to ‘Trajectory” tab and change the “Color Scale Range” to -10 to 10 (or other values like -1 to 1) g. Save to image by clicking “File” --> Render
Alternatively, the ABPS web services also provide a direct visualization tool.
For example,
http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/visualize.cgi?jobid=14556524059
More examples using VMD can be found at a APBS website, starting at Step 16.
This mapping of the electrostatic potentials should work on a LINUX box, but I have not tested on any machine running Windows.