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Binding energies
Ionic strength dependence of peptide-RNA interactions
Data analysis Python script
Peptide
RNA
RNA-peptide complex
Parallel execution for large problems
pKa calculations
Lysozyme pKa example
Potentials of mean force
Poisson–Boltzmann profile for an ion channel
The polar solvation potential of mean force for a helix in a dielectric slab membrane
Solvation energies
The Born ion
Visualization
APBS electrostatics in PyMOL
APBS electrostatics in VMD
APBS electrostatics on the web
Frequently-asked questions
How do I calculate a binding energy?
How do I calculate a pKa?
How do I calculate a solvation energy?
How do I calculate solvation forces?
How do I get my structures ready for electrostatics calculations?
How do I model the inhomogeneous environment of a membrane?
How do I run a calculation that's too big for my computer?
How do I run my calculations on someone else's computer?
How do I use APBS with my external simulation software?
How do I visualize the electrostatic potential?
What are the sources of error in my calculation?
What are the units of electrostatic potential?
What is FEtk?
What is focusing?
What is MALOC?
What is Opal?
What is PMG?
Getting help
License
Programmer's guide
Related software
Release history
Alpha releases
Version 0.1.0 (2001-08)
Version 0.1.1 (2001-08)
Version 0.1.2 (2001-09)
Version 0.1.3 (2001-09)
Version 0.1.4 (2001-09)
Version 0.1.5 (2009-10)
Version 0.1.6 (2001-11)
Version 0.1.7 (2001-12)
Version 0.1.8 (2002-01)
Beta releases
Version 0.2.0 (2002-03)
Version 0.2.1 (2002-04)
Version 0.2.2 (2002-08)
Version 0.2.3 (2002-10)
Version 0.2.4 (2002-10)
Version 0.2.5 (2002-11)
Version 0.2.6 (2003-01)
Version 0.3.0 (2004-02)
Version 0.3.1 (2004-04)
Version 0.3.2 (2004-11)
Version 0.4.0 (2005-12)
Version 0.5.0 (2007-01)
Version 0.5.1 (2007-07)
Version 1.0.0 (2008-04)
Version 1.1.0 (2009-03)
Version 1.2.0 (2009-10)
Version 1.2.1 (2009-12)
Supporting organizations
User guide
Customizing and expanding APBS
Installation and availability
Binary installation
Source installation
Subversion
Package overview
Running APBS
Input files
APOLAR input file section
APOLAR keywords
bconc
calcenergy
calcforce
dpos
gamma
grid
mol
press
sdens
srad
srfm
swin
temp
Basic APOLAR calculations
ELEC input file section
ELEC block naming
ELEC keywords
akeyPRE
akeySOLVE
async
bcfl
calcenergy
calcforce
cgcent
cglen
chgm
dime
domainLength
ekey
etol
fgcent
fglen
gcent
glen
grid
ion
lpbe
lrpbe
maxsolve
maxvert
mol
nlev
npbe
nrpbe
ofrac
pdie
pdime
sdens
sdie
smpbe
srad
srfm
swin
targetNum
targetRes
temp
useaqua
usemap
usemesh
write
writemat
Types of ELEC calculations
fe-manual: manually-configured adaptive finite element Poisson-Boltzmann calculations
mg-auto: automatically-configured sequential focusing multigrid Poisson-Boltzmann calculations
mg-dummy: calculations of surface and charge distribution properties which do not require solution of the PBE
mg-manual: manually-configured multigrid Poisson-Boltzmann calculations
mg-para: automatically-configured parallel focusing multigrid Poisson-Boltzmann calculations
PRINT input file section
READ input file section
READ examples
READ keywords
charge
diel
kappa
mesh
mol
parm
pot
Invocation
APBS command-line binary
APBS Opal client
Using APBS with other programs
Utilities
Mesh Tools
del2dx
dxmath
mergedx2
Developers
Documentation sandbox
pKa prediction using PDB2PKA (EXPERIMENTAL)
Where is the best place to eat breakfast in the Central West End?
Task lists
New APBS documentation
New PDB2PQR documentation
File formats
Matrices
Harwell-Boeing
Mesh and data
MCSF finite element
OpenDX scalar data
UHBD
Molecular structure
MOL2
PDB
PQR
XML
Parameter files
APBS flat-file format
APBS XML format
PDB2PQR XML format
PDB2PQR
Citing your use of PDB2PQR
Contributors
Downloads and web servers
Downloads
Web servers
Examples
Assigning titration states with PROPKA
Basic PDB file operations
Ligand parameterization
Running APBS through the PDB2PQR web portal
Frequently-asked questions
Can I add my own charge and radius parameters to PDB2PQR?
Can PDB2PQR output create a PQR file using forcefield-specific residue and atom names?
Does the input PDB file need to be in a specific format?
How do I add my own functionality to PDB2PQR?
How is PDB2PQR licensed?
I already know the protonation state of a residue. How can I make PDB2PQR aware of it?
What causes the following warning: "WARNING: PDB2PQR was unable to assign charges to the following atoms"?
What causes the following warning: "WARNING: PDB2PQR was unable to assign charges to the following atoms"?
What force fields or parameter sets are available?
What is a PQR file?
What is PEOE_PB?
What is PROPKA?
What platforms, compilers, and architectures are compatible with PDB2PQR?
Can I run PDB2PQR under Windows?
What types of residues can PDB2PQR recognize?
Why are chain IDs not included in the output by default?
Getting help
License
Programmer's guide
Adding user-defined functions to PDB2PQR
Adding User-Defined Functions via the Extensions directory
API documentation
Atom and residue naming scheme
Canonical naming scheme
Python file documentation
Using XML Files and Regular Expressions
Related software
Release history
Beta releases
Version 1.0.0 (2005-08)
Version 1.0.1 (2005-10)
Version 1.0.2 (2005-12)
Version 1.1.0 (2006-04)
Version 1.1.1 (2006-05)
Version 1.1.2 (2006-06)
Version 1.2.0 (2007-01)
Version 1.2.1 (2007-04)
Version 1.3.0 (2008-01)
Version 1.4.0 (2009-03)
Version 1.5 (2009-10)
Version 1.6
Supporting organizations
User guide
Algorithm description
Further reading
Installation and availability
Subversion
Limitations
Using PDB2PQR
Tutorials
Assigning titration states with PROPKA
Born ion solvation energy
Parameterizing ligands in electrostatics calculations
Parameterizing PDB files
Running APBS through the PDB2PQR web portal
Running electrostatics calculations in parallel
Visualizing and calculating APBS electrostatics in PyMOL
Visualizing and calculating APBS electrostatics in VMD
Workshops and courses
BII workshop tutorials
CCPB workshop tutorials
NBCR workshop tutorials
Sitemap
Recent site activity
Source installation
edited by Nathan Baker
What is FEtk?
edited by Nathan Baker
What are the units of electrostatic potential?
edited by Nathan Baker
The polar solvation potential of mean force for a helix in a dielectric slab membrane
attachment from Yong Huang
attachment removed by Yong Huang
NBCR workshop tutorials
edited by Nathan Baker
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APBS
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Programmer's guide
The latest APBS Programmer's Guide is attached below.
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programmer.pdf
- on Mar 7, 2010 8:13 AM by Nathan Baker (version 1)
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