How to perform APBS calculations

(please see click for Yang lab website)

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.