Hi all,

I have installed apbs via Synaptec on Ubuntu 9.10. "apbs --version" reports itself as 1.1.0 and there seems to be a page describing it here (although I do not see explicit details about how it was compiled):

https://launchpad.net/ubuntu/+source/apbs/1.1.0-1 

When I run a standard calculation via the PyMOL APBS plugin (full input file pasted at the end of this email), I say

...
elec
    mg-auto
    ...
    write pot dx pymol-generated
end

And the output file is called pymol-generated-PE0.dx. On most systems, the output file is pymol-generated.dx. I need to know what it'll be called in order for the plugin to work properly. Is there some way to either 1. specify the full output name or 2. know for certain what it'll be? The plugin can interrogate apbs via a call to "apbs --version" or something similar if it has to.

I've pasted

1. The full input file
2. The full output from APBS (it first says it'll spit out pymol-generated.dx and then changes its mind after calculating forces)

Thanks!

-Michael

P.S. I'll update the APBS input file for the next release of the plugin. You'll note that it complains about me using the old syntax below.

------ 1. Begin pymol-generated.in ------

mglerner@mglerner-ubuntu9:~$ cat pymol-generated.in 
#
# Note that most of the comments here were taken from sample
# input files that came with APBS.  You can find APBS at
# http://agave.wustl.edu/apbs/
# Note that APBS is GPL'd code.
#
read
    mol pqr pymol-generated.pqr       # read molecule 1
end
elec
    mg-auto
    dime   129 129 129  # number of find grid points
                     # calculated by psize.py
    cglen   48.448301 61.053799 65.009700 # coarse mesh lengths (A)
    fglen   48.448301 55.914000 58.241000 # fine mesh lengths (A)
                     # calculated by psize.py
    cgcent 44.103500 43.315000 -9.435500  # (could also give (x,y,z) form psize.py) #known center
    fgcent 44.103500 43.315000 -9.435500  # (could also give (x,y,z) form psize.py) #known center
    lpbe               # solve the full nonlinear PBE with npbe
    #lpbe            # solve the linear PBE with lpbe
    bcfl sdh          # Boundary condition flag
                     #  0 => Zero
                     #  1 => Single DH sphere
                     #  2 => Multiple DH spheres
                     #  4 => Focusing
                     #
    #ion 1 0.000 2.0 # Counterion declaration:
    ion  1 0.150000 2.000000     # Counterion declaration:
    ion -1 0.150000 1.800000     # ion <charge> <conc (M)> <radius>
    ion  2 0.000000 2.000000     # ion <charge> <conc (M)> <radius>
    ion -2 0.000000 2.000000     # ion <charge> <conc (M)> <radius>
    pdie 2.000000          # Solute dielectric
    sdie 78.000000          # Solvent dielectric
    chgm spl2          # Charge disc method
                     # 0 is linear splines
                     # 1 is cubic b-splines
    mol 1            # which molecule to use
    srfm smol        # Surface calculation method
                     #  0 => Mol surface for epsilon;
                     #       inflated VdW for kappa; no
                     #       smoothing
                     #  1 => As 0 with harmoic average
                     #       smoothing
                     #  2 => Cubic spline 
    srad 1.400000          # Solvent radius (1.4 for water)
    swin 0.3         # Surface cubic spline window .. default 0.3
    temp 310.000000          # System temperature (298.15 default)
    sdens 10.000000         # Specify the number of grid points per square-angstrom to use in Vacc object. Ignored when srad is 0.0 (see srad) or srfm is spl2 (see srfm). There is a direct correlation between the value used for the Vacc sphere density, the accuracy of the Vacc object, and the APBS calculation time. APBS default value is 10.0.
    gamma 0.105      # Surface tension parameter for apolar forces (in kJ/mol/A^2)
                     # only used for force calculations, so we don't care, but
                     # it's always required, and 0.105 is the default
    calcenergy no    # Energy I/O to stdout
                     #  0 => don't write out energy
                     #  1 => write out total energy
                     #  2 => write out total energy and all
                     #       components
    calcforce no     # Atomic forces I/O (to stdout)
                     #  0 => don't write out forces
                     #  1 => write out net forces on molecule
                     #  2 => write out atom-level forces
    write pot dx pymol-generated  # What to write .. this says write the potential in dx
                     # format to a file.
end
quit


------- 1. End pymol-generated.in -------

------ 2. Begin output ------

mglerner@mglerner-ubuntu9:~$ apbs pymol-generated.in 


----------------------------------------------------------------------
APBS -- Adaptive Poisson-Boltzmann Solver
Version 1.1.0
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) 2002-2009, Washington University in St. Louis.
Portions Copyright (c) 2002-2009.  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 Aug  3 2009 at 15:37:31

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:  If you are using PyMOL or VMD and still seeing this message,
parseMG:  please contact the developers of those programs regarding this message.
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.
  1564 atoms
  Centered at (4.424e+01, 4.315e+01, -9.332e+00)
  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:  7.98362 A
  Current memory usage:  471.508 MB total, 471.508 MB high water
  Using cubic spline charge discretization.
  Grid dimensions: 129 x 129 x 129
  Grid spacings: 0.379 x 0.477 x 0.508
  Grid lengths: 48.448 x 61.054 x 65.010
  Grid center: (44.103, 43.315, -9.435)
  Multigrid levels: 6
  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:  471.693 MB total, 494.212 MB high water
  Using cubic spline charge discretization.
  Grid dimensions: 129 x 129 x 129
  Grid spacings: 0.379 x 0.437 x 0.455
  Grid lengths: 48.448 x 55.914 x 58.241
  Grid center: (44.103, 43.315, -9.435)
  Multigrid levels: 6
  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 pymol-generated.dx
  Solving PDE (see io.mc* for details)...
  Calculating energy (see io.mc* for details)...
  Calculating forces...
  Writing potential to pymol-generated-PE0.dx
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying 1 molecules
Final memory usage:  0.370 MB total, 494.212 MB high water


Thanks for using APBS!


------- 2. End output -------

--
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)