Software
To use APBS to calculate an electrostatic surface potential within pymol do the following:
1) Open a pymol session by typing "pymol" at the unix prompt. A window will appear like this:
.png)
2) Load your coordinate set by clicking on the "File" menu, then "Open...". Browse for your coordinate file. In this example, I am using helix.pdb.
.png)
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3) Click on the "Plugin" menu, then select "APBS Tools2.1".
.
4) A widow will pop up like this:
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And a message is printed to the screen like this:
Running:
prog=/joule2/programs/pymol/pymol_v1.4/pymol-v1.4-Linux-x86/freemol/bin/apbs.exe
args=('/joule2/programs/pymol/pymol_v1.4/pymol-v1.4-Linux-x86/freemol/bin/apbs.exe', '--version')
Results were:
Return value: 13
Output:
APBS 1.3
----------------------------------------------------------------------
APBS -- Adaptive Poisson-Boltzmann Solver
Version 1.3
Nathan A. Baker (nathan.baker@pnl.gov)
Washington University in St. Louis
Additional contributing authors listed in the code documentation.
Copyright (c) 2010, Pacific Northwest National Laboratory. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst.
All rights reserved.
...some legal terms omited for brevity...
----------------------------------------------------------------------
APBS uses FETK (the Finite Element ToolKit) to solve the
Poisson-Boltzmann equation numerically. FETK is a portable collection
of finite element modeling class libraries developed by the Michael Holst
research group and written in an object-oriented form of C. FEtk is
designed to solve general coupled systems of nonlinear partial differential
equations using adaptive finite element methods, inexact Newton methods,
and algebraic multilevel methods. More information about FEtk may be found
at <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
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.
This executable compiled on Oct 21 2010 at 10:49:41
5) Click the button "Set grid" in the window displayed above. Charges will be calcualted with PDB2PQR. There will be no change in the appearance of the molecule yet. The time required for the calculation may be a few seconds or minutes depending on how many atoms are in the coordinate file. Some message will print to the screen like this:
GENERATING PQR FILE via PDB2PQR
Erasing contents of /tmp/pymol-generated.pdb in order to generate new PDB file
Erasing contents of /tmp/pymol-generated.pdb in order to clean it up
TESTING
DONE TESTING
Appended /joule2/programs/pymol/pymol_v1.4/pymol-v1.4-Linux-x86/freemol/share
Appended /joule2/programs/pymol/pymol_v1.4/pymol-v1.4-Linux-x86/freemol/share/pdb2pqr
Imported pdb2pqr
args are: ('/joule2/programs/pymol/pymol_v1.4/pymol-v1.4-Linux-x86/freemol/share/pdb2pqr/pdb2pqr.py', '--ff=AMBER', '/tmp/pymol-generated.pdb', '/tmp/pymol-generated.pqr')
Imported main
--------------------------
PDB2PQR - a Python-based structural conversion utility
--------------------------
Please cite your use of PDB2PQR as:
Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA.
PDB2PQR: an automated pipeline for the setup, execution,
and analysis of Poisson-Boltzmann electrostatics calculations.
Nucleic Acids Research 32 W665-W667 (2004).
PDB2PQR's mainCommand returned None
Erasing contents of /tmp/pymol-generated.pqr in order to clean it up
I WILL RETURN TRUE from pdb2pqr
GENERATED
APBS's psize.py was used to calculated grid dimensions
Estimated memory usage 13.5011672974 MB out of maximum allowed 1500.0
APBS Tools: coarse grid: (34.888,22.484,19.514)
APBS Tools: fine grid: (34.888,22.484,19.514)
APBS Tools: center: (6.682,4.609,2.248)
APBS Tools: fine grid points (65,33,33)
6) In the same window as above, click the "Run APBS" button. You will get a window like this:
.
And a message will be printed to the screen like this:
GOT THE APBS INPUT FILE
Erasing contents of /tmp/pymol-generated.in in order to write new input file
GENERATING PQR FILE via PDB2PQR
Erasing contents of /tmp/pymol-generated.pdb in order to generate new PDB file
Erasing contents of /tmp/pymol-generated.pdb in order to clean it up
TESTING
DONE TESTING
Appended /joule2/programs/pymol/pymol_v1.4/pymol-v1.4-Linux-x86/freemol/share
Appended /joule2/programs/pymol/pymol_v1.4/pymol-v1.4-Linux-x86/freemol/share/pdb2pqr
Imported pdb2pqr
args are: ('/joule2/programs/pymol/pymol_v1.4/pymol-v1.4-Linux-x86/freemol/share/pdb2pqr/pdb2pqr.py', '--ff=AMBER', '/tmp/pymol-generated.pdb', '/tmp/pymol-generated.pqr')
Imported main
--------------------------
PDB2PQR - a Python-based structural conversion utility
--------------------------
Please cite your use of PDB2PQR as:
Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA.
PDB2PQR: an automated pipeline for the setup, execution,
and analysis of Poisson-Boltzmann electrostatics calculations.
Nucleic Acids Research 32 W665-W667 (2004).
PDB2PQR's mainCommand returned None
Erasing contents of /tmp/pymol-generated.pqr in order to clean it up
I WILL RETURN TRUE from pdb2pqr
GENERATED
Running:
prog=/joule2/programs/pymol/pymol_v1.4/pymol-v1.4-Linux-x86/freemol/bin/apbs.exe
args=('/joule2/programs/pymol/pymol_v1.4/pymol-v1.4-Linux-x86/freemol/bin/apbs.exe', '/tmp/pymol-generated.in')
Results were:
Return value: 0
Output:
----------------------------------------------------------------------
APBS -- Adaptive Poisson-Boltzmann Solver
Version 1.3
Nathan A. Baker (nathan.baker@pnl.gov)
Washington University in St. Louis
Additional contributing authors listed in the code documentation.
...more legal terms omited for brevity...
This executable compiled on Oct 21 2010 at 10:49:41
Parsing input file /tmp/pymol-generated.in...
Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from /tmp/pymol-generated.pqr.
103 atoms
Centered at (6.595e+00, 4.659e+00, 2.248e+00)
Net charge 1.69e-15 e
Preparing to run 2 PBE calculations.
----------------------------------------
CALCULATION #1: MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 7.98362 A
Current memory usage: 17.780 MB total, 17.780 MB high water
Using cubic spline charge discretization.
Grid dimensions: 65 x 33 x 33
Grid spacings: 0.545 x 0.703 x 0.610
Grid lengths: 34.888 x 22.484 x 19.514
Grid center: (6.682, 4.609, 2.248)
Multigrid levels: 4
Molecule ID: 1
Linearized traditional PBE
Single Debye-Huckel sphere boundary conditions
4 ion species (0.150 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.150 M concentration
1.800 A-radius, -1.000 e-charge, 0.150 M concentration
2.000 A-radius, 2.000 e-charge, 0.000 M concentration
2.000 A-radius, -2.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 310.000 K
Solving PDE (see io.mc* for details)...
Calculating energy (see io.mc* for details)...
Calculating forces...
----------------------------------------
CALCULATION #2: MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 7.98362 A
Current memory usage: 17.780 MB total, 19.685 MB high water
Using cubic spline charge discretization.
Grid dimensions: 65 x 33 x 33
Grid spacings: 0.545 x 0.703 x 0.610
Grid lengths: 34.888 x 22.484 x 19.514
Grid center: (6.682, 4.609, 2.248)
Multigrid levels: 4
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
4 ion species (0.150 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.150 M concentration
1.800 A-radius, -1.000 e-charge, 0.150 M concentration
2.000 A-radius, 2.000 e-charge, 0.000 M concentration
2.000 A-radius, -2.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 310.000 K
Potential to be written to /tmp/pymol-generated.dx
Solving PDE (see io.mc* for details)...
Calculating energy (see io.mc* for details)...
Calculating forces...
Writing potential to /tmp/pymol-generated.dx
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying 1 molecules
Final memory usage: 0.001 MB total, 19.685 MB high water
Thanks for using APBS!
ObjectMapLoadDXFile: Loading from '/tmp/pymol-generated.dx'.
DXStrToMap: Dimensions: 65 33 33
DXStrToMap: Origin -10.762 -6.633 -7.510
DXStrToMap: Grid 0.545 0.703 0.610
DXStrToMap: 70785 data points.
7) Show the molecular surface by clicking the "Show" button in the box labeled "Molecular Surface". The electrostatic surface potential will be mapped onto the molecular surface in a representation like this:
.png)
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8) You can make the colors more or less saturated by changing the upper and lower limits of the charge range. Adjust the up/down buttons for "Low" and "High" in the "Molecular Surface" window. Then click the "Show" button again, in the same window. I changed the values to +3 and -3 to get the following image:
.
