Hi Roland,

I tried your example with PyMOL APBS Tools, this shouldn't be a complicated one. A few questions for you:

1. Can you tell us the full path of your apbs binary?

2. In PyMOL APBS Tools, under "Temporary File Locations", can you send us a screenshot showing your temporary file locations?

Thanks,

Yong


On Thu, Dec 25, 2008 at 5:37 AM, Roland Schmucki <roland.schmucki@gmail.com> wrote:
Hello, Nathan

Here is the input file *.in

Thank you for your consideration.

Kind regards,

Roland Schmucki
PhD student
Institute of Biophysical Chemistry
Goethe-University Frankfurt am Main, Germany



Nathan Baker wrote:
Hello --

Could you please attach the PyMOL-generated APBS input file as well?

Thanks,

Nathan

On Tue, Dec 23, 2008 at 4:46 PM, Roland Schmucki <roland.schmucki@gmail.com> wrote:
Hello !

I am using PyMol on a computer with Windows Vista.

I have prepared a pdb- and pqr-file (attached). Now, I'd like to make
the potential surface plot by using the APBS plugin in PyMol. I have
downloaded the APBS binary and specified the correct path in the PyMol
APBS Tools menu. In addition, I have set the option (Main options in
PyMol APBS Tools) so that my own pqr file is used.

Now, after "Set grid" and "Run APBS" the following error message
appears in the console:

APBS Tools: set pqr file to C:\Users\Roland\Desktop\polyB-Hamada\polyB-Opalp.pqr
cs [4, 2, 2]
finedim [63.161001205444336, 30.231099987030028, 30.479299831390382]
nlev 4
mult_fac 32
finegridpoints [129, 65, 65]
 APBS Tools: coarse grid: (73.374,30.231,30.479)
 APBS Tools: fine grid: (63.161,30.231,30.479)
 APBS Tools: center: (2.391,0.702,0.251)
 APBS Tools: fine grid points (129,65,65)
ObjectMapLoadDXFile-Error: Unable to open file!
ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist?

I have searched the archives of the mailing lists for PyMol, APBS, and
also the "Troubleshooting" section at the bottom of this page:
http://www.pymolwiki.org/index.php/APBS but could not find a solution
yet.

I would appreciate any suggestion and help.

Thank you very much.

Roland Schmucki
PhD student
Institute of Biophysical Chemistry
Goethe-University Frankfut am Main, Germany

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Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/


#
# 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 C:\Users\Roland\Desktop\polyB-Hamada\polyB-Opalp.pqr       # read molecule 1
end
elec
   mg-auto
   dime   129 65 65  # number of find grid points
                    # calculated by psize.py
   cglen   73.373702 30.231100 30.479300 # coarse mesh lengths (A)
   fglen   63.161001 30.231100 30.479300 # fine mesh lengths (A)
                    # calculated by psize.py
   cgcent 2.390500 0.701500 0.250500  # (could also give (x,y,z) form psize.py) #known center
   fgcent 2.390500 0.701500 0.250500  # (could also give (x,y,z) form psize.py) #known center
   npbe               # 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 0.000000 2.000000     # Counterion declaration:
   ion -1 0.000000 2.000000     # 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 80.000000          # 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


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Yong Huang, D.Sc.

Center for Computational Biology
Washington University School of Medicine