jlara@jlara:~$ pymol
 PyMOL(TM) Molecular Graphics System, Version 1.1beta3.
 Copyright (C) 2007 by DeLano Scientific LLC.
 All Rights Reserved.
 
    Created by Warren L. DeLano, Ph.D. 
 
    Other Major Authors and Contributors:

       Ralf W. Grosse-Kunstleve, Ph.D.
 
    PyMOL is user-supported open-source software.  Although some versions
    are freely available, PyMOL is not in the public domain.
 
    If PyMOL is helpful in your work or study, then please volunteer 
    support for our ongoing efforts to create open and affordable scientific
    software by purchasing a PyMOL Maintenance and/or Support subscription.

    More information can be found at "http://www.pymol.org".
 
    Enter "help" for a list of commands.
    Enter "help <command-name>" for information on a specific command.

 Hit ESC anytime to toggle between text and graphics.

 OpenGL graphics engine:
  GL_VENDOR: ATI Technologies Inc.
  GL_RENDERER: Radeon X1300/X1550 Series
  GL_VERSION: 2.1.8087 Release
 Detected 2 CPU cores.  Enabled multithreaded rendering.
HEADER    HYDROLASE                               20-AUG-99   1CU1
TITLE     CRYSTAL STRUCTURE OF AN ENZYME COMPLEX FROM HEPATITIS C
TITLE    2 VIRUS
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: PROTEIN (PROTEASE/HELICASE NS3);
COMPND   3 CHAIN: A, B;
COMPND   4 EC: 3.4.21.-;
COMPND   5 ENGINEERED: YES
 ObjectMolecule: Read secondary structure assignments.
 ObjectMolecule: Read crystal symmetry information.
 Symmetry: Found 4 symmetry operators.
 CmdLoad: "/tmp/1CU1.pdb" loaded as "1CU1".
cs [9, 6, 7]
finedim [128.06400108337402, 95.163002014160156, 106.77799987792969]
nlev 4
mult_fac 32
finegridpoints [289, 193, 225]
Maximum number of grid points exceeded.  Old grid dimensions were [289, 193, 225]
Fine grid points rounded down from [133, 89, 103]
New grid dimensions are [129, 65, 97]
 APBS Tools: coarse grid: (183.709,127.777,147.523)
 APBS Tools: fine grid: (128.064,95.163,106.778)
 APBS Tools: center: (23.062,66.456,110.576)
 APBS Tools: fine grid points (129,65,97)


----------------------------------------------------------------------
	APBS -- Adaptive Poisson-Boltzmann Solver
	Version 1.0.0
	
	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) 2002-2008, Washington University in St. Louis.
	Portions Copyright (c) 2002-2008.  Nathan A. Baker
	Portions Copyright (c) 1999-2002.  The Regents of the University of California.
	Portions Copyright (c) 1995.  Michael Holst
	
	All rights reserved.
	
	Redistribution and use in source and binary forms, with or without
	modification, are permitted provided that the following conditions are met: 
	
	* Redistributions of source code must retain the above copyright notice, this
	list of conditions and the following disclaimer.  
	
	* Redistributions in binary form must reproduce the above copyright notice,
	this list of conditions and the following disclaimer in the documentation
	and/or other materials provided with the distribution.
	
	* Neither the name of Washington University in St. Louis nor the names of its
	contributors may be used to endorse or promote products derived from this
	software without specific prior written permission.
	
	THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
	"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
	LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
	A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
	CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
	EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
	PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
	PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
	LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
	NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
	SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
----------------------------------------------------------------------
	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  8 2008 at 15:58:43

Parsing input file pymol-generated.in...
NOsh:  Deprecated use of ION keyword! Use key-value pairs
NOsh:  Deprecated use of ION keyword! Use key-value pairs
NOsh:  Deprecated use of ION keyword! Use key-value pairs
NOsh:  Deprecated use of ION keyword! Use key-value pairs
parseMG:  GAMMA keyword deprecated!
parseMG:  Please see new APOLAR documentation.
Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from pymol-generated.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
  19190 atoms
  Centered at (2.291e+01, 6.646e+01, 1.104e+02)
  Net charge 2.00e+00 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:  0 A
  Current memory usage:  259.571 MB total, 259.571 MB high water
  Using cubic spline charge discretization.
  Grid dimensions: 129 x 65 x 97
  Grid spacings: 1.435 x 1.997 x 1.537
  Grid lengths: 183.709 x 127.777 x 147.523
  Grid center: (23.062, 66.456, 110.576)
  Multigrid levels: 4
  Molecule ID: 1
  Nonlinear traditional PBE
  Single Debye-Huckel sphere boundary conditions
  4 ion species (0.000 M ionic strength):
    2.000 A-radius, 1.000 e-charge, 0.000 M concentration
    2.000 A-radius, -1.000 e-charge, 0.000 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: 80.000
  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:  0 A
  Current memory usage:  261.840 MB total, 300.658 MB high water
  Using cubic spline charge discretization.
  Grid dimensions: 129 x 65 x 97
  Grid spacings: 1.001 x 1.487 x 1.112
  Grid lengths: 128.064 x 95.163 x 106.778
  Grid center: (23.062, 66.456, 110.576)
  Multigrid levels: 4
  Molecule ID: 1
  Nonlinear traditional PBE
  Boundary conditions from focusing
  4 ion species (0.000 M ionic strength):
    2.000 A-radius, 1.000 e-charge, 0.000 M concentration
    2.000 A-radius, -1.000 e-charge, 0.000 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: 80.000
  Using "molecular" surface definition;harmonic average smoothing
  Solvent probe radius: 1.400 A
  Temperature:  310.000 K
  Potential to be written to pymol-generated.dx
  Solving PDE (see io.mc* for details)...
  Calculating energy (see io.mc* for details)...
  Calculating forces...
  Writing potential to 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:  4.539 MB total, 300.658 MB high water


Thanks for using APBS!

 ObjectMapLoadDXFile: Loading from 'pymol-generated.dx'.
 DXStrToMap: Dimensions: 129 65 97
 DXStrToMap: Origin  -40.970   18.874   57.187
 DXStrToMap: Grid    1.000    1.487    1.112
 DXStrToMap: 813345 data points.
CmdException Exception in Tk callback
  Function: <bound method VisualizationGroup.showPosSurface of <pmg_tk.startup.apbs_tools.VisualizationGroup instance at 0xa7f42cc>> (type: <type 'instancemethod'>)
  Args: ()
Traceback (innermost last):
  File "/usr/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__
    return apply(self.func, args)
  File "/var/lib/python-support/python2.5/pmg_tk/startup/apbs_tools.py", line 658, in showPosSurface
    self.updatePosSurface()
  File "/var/lib/python-support/python2.5/pmg_tk/startup/apbs_tools.py", line 663, in updatePosSurface
    pymol.cmd.isosurface('iso_pos',self.map.getvalue(),float(self.pos_surf_val.getvalue()))
  File "/var/lib/python-support/python2.5/pymol/creating.py", line 526, in isosurface
    if _self._raising(r,_self): raise pymol.CmdException
CmdException: <pymol.CmdException instance at 0xbf812ec>
CmdException Exception in Tk callback
  Function: <bound method VisualizationGroup.showPosSurface of <pmg_tk.startup.apbs_tools.VisualizationGroup instance at 0xa7f42cc>> (type: <type 'instancemethod'>)
  Args: ()
Traceback (innermost last):
  File "/usr/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__
    return apply(self.func, args)
  File "/var/lib/python-support/python2.5/pmg_tk/startup/apbs_tools.py", line 658, in showPosSurface
    self.updatePosSurface()
  File "/var/lib/python-support/python2.5/pmg_tk/startup/apbs_tools.py", line 663, in updatePosSurface
    pymol.cmd.isosurface('iso_pos',self.map.getvalue(),float(self.pos_surf_val.getvalue()))
  File "/var/lib/python-support/python2.5/pymol/creating.py", line 526, in isosurface
    if _self._raising(r,_self): raise pymol.CmdException
CmdException: <pymol.CmdException instance at 0xbf812ec>

CmdException Exception in Tk callback
  Function: <bound method VisualizationGroup.showNegSurface of <pmg_tk.startup.apbs_tools.VisualizationGroup instance at 0xa7f42cc>> (type: <type 'instancemethod'>)
  Args: ()
Traceback (innermost last):
  File "/usr/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__
    return apply(self.func, args)
  File "/var/lib/python-support/python2.5/pmg_tk/startup/apbs_tools.py", line 667, in showNegSurface
    self.updateNegSurface()
  File "/var/lib/python-support/python2.5/pmg_tk/startup/apbs_tools.py", line 672, in updateNegSurface
    pymol.cmd.isosurface('iso_neg',self.map.getvalue(),float(self.neg_surf_val.getvalue()))
  File "/var/lib/python-support/python2.5/pymol/creating.py", line 526, in isosurface
    if _self._raising(r,_self): raise pymol.CmdException
CmdException: <pymol.CmdException instance at 0xbf810ac>





jlara@jlara:~$ apbs quicktest


----------------------------------------------------------------------
	APBS -- Adaptive Poisson-Boltzmann Solver
	Version 1.0.0
	
	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) 2002-2008, Washington University in St. Louis.
	Portions Copyright (c) 2002-2008.  Nathan A. Baker
	Portions Copyright (c) 1999-2002.  The Regents of the University of California.
	Portions Copyright (c) 1995.  Michael Holst
	
	All rights reserved.
	
	Redistribution and use in source and binary forms, with or without
	modification, are permitted provided that the following conditions are met: 
	
	* Redistributions of source code must retain the above copyright notice, this
	list of conditions and the following disclaimer.  
	
	* Redistributions in binary form must reproduce the above copyright notice,
	this list of conditions and the following disclaimer in the documentation
	and/or other materials provided with the distribution.
	
	* Neither the name of Washington University in St. Louis nor the names of its
	contributors may be used to endorse or promote products derived from this
	software without specific prior written permission.
	
	THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
	"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
	LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
	A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
	CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
	EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
	PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
	PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
	LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
	NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
	SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
----------------------------------------------------------------------
	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  8 2008 at 15:58:43

Parsing input file quicktest...
Vio_ctor2: some error occurred.
Vio_ctor: Vio_ctor2() failed.
Error while opening input file quicktest!