

----------------------------------------------------------------------
	APBS -- Adaptive Poisson-Boltzmann Solver
	Version 0.5.1
	
	Nathan A. Baker (baker@biochem.wustl.edu)
	Dept. Biochemistry and Molecular Biophysics
	Center for Computational Biology
	Washington University in St. Louis
	
	Additional contributing authors listed in the code documentation.
	
	Copyright (c) 2002-2007.  Washington University in St. Louis.
	All Rights Reserved.
	Portions Copyright (c) 1999-2002.  The Regents of the University of 
	California.
	Portions Copyright (c) 1995.  Michael Holst.
	
	This program is free software; you can redistribute it and/or modify
	it under the terms of the GNU General Public License as published by
	the Free Software Foundation; either version 2 of the License, or
	(at your option) any later version.
	
	This program is distributed in the hope that it will be useful,
	but WITHOUT ANY WARRANTY; without even the implied warranty of
	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
	GNU General Public License for more details.
	
	You should have received a copy of the GNU General Public License
	along with this program; if not, write to the Free Software
	Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307 USA
	
	Linking APBS statically or dynamically with other modules is making a
	combined work based on APBS. Thus, the terms and conditions of the GNU
	General Public License cover the whole combination.
	
	SPECIAL GPL EXCEPTION
	In addition, as a special exception, the copyright holders of APBS
	give you permission to combine the APBS program with free software
	programs and libraries that are released under the GNU LGPL or with
	code included in releases of ISIM, Ion Simulator Interface, PMV,
	SMOL, VMD, and Vision. Such combined software may be linked with APBS and
	redistributed together in original or modified form as mere aggregation
	without requirement that the entire work be under the scope of the GNU
	General Public License. This special exception permission is also extended
	to any software listed in the SPECIAL GPL EXCEPTION clauses by the PMG,
	FEtk, MC, or MALOC libraries.
	
	Note that people who make modified versions of APBS are not obligated
	to grant this special exception for their modified versions; it is
	their choice whether to do so. The GNU General Public License gives
	permission to release a modified version without this exception; this
	exception also makes it possible to release a modified version which
	carries forward this exception.
----------------------------------------------------------------------
	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 written in an object-oriented
	version of C.  It 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>.
----------------------------------------------------------------------
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 Sep 12 2007 at 10:43:13

Parsing input file solvation-apbs-vac.in...
Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from 2ala.pqr.
  22 atoms
  Centered at (4.112e+00, 4.824e+00, -6.205e-01)
  Net charge -2.78e-17 e
Preparing to run 2 PBE calculations.
----------------------------------------
CALCULATION #1 (elec): MULTIGRID
  Setting up problem...
  Using cubic spline charge discretization.
  Grid dimensions: 33 x 33 x 33
  Grid spacings: 0.500 x 0.500 x 0.500
  Grid lengths: 16.000 x 16.000 x 16.000
  Grid center: (4.112, 4.824, -0.620)
  Multigrid levels: 4
  Molecule ID: 1
  Linearized traditional PBE
  Single Debye-Huckel sphere boundary conditions
  0 ion species (0.000 M ionic strength):
  Solute dielectric: 2.000
  Solvent dielectric: 1.000
  Using spline-based surface definition;window = 0.300
  Temperature:  298.150 K
  Electrostatic energies will be calculated
  All-atom solvent forces will be calculated
----------------------------------------
CALCULATION #2 (npolar): APOLAR
----------------------------------------
PRINT STATEMENTS

print energy 1 (elec) end
  Local net energy (PE 0) = 1.089755873935E+03 kJ/mol
  Global net ELEC energy = 1.089755873935E+03 kJ/mol

print APOL energy 1 (npolar) end
  Global net APOL energy = 4.148317453106E+01 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Final memory usage:  8.454 MB total, 8.664 MB high water


Thanks for using APBS!

