Thread: [Apbs-users] APBS Tool for VMD
Biomolecular electrostatics software
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From: Andreas K. <a....@he...> - 2007-08-29 13:53:49
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Hi everybody, When I try out the same example as in the tutorial 'How do I visualize the electrostatic potential around by biomolecule' using the 1MYK pdb file I get the following error messages (see ****): > apbsrun) Running job mode=normal > apbsrun) dir is C:/Documents and Settings/lfsqak/My Documents/temp/apbs.42662 > apbsrun) using VMD radii > apbsrun) using pqrplugin for C:/Documents and Settings/lfsqak/My Documents/temp/ > apbs.42662/test.pqr > Info) Opened coordinate file C:/Documents and Settings/lfsqak/My Documents/temp/ > apbs.42662/test.pqr for writing. > apbsrun) Output files pot > Info) Finished with coordinate file C:/Documents and Settings/lfsqak/My Document > s/temp/apbs.42662/test.pqr. > ---------------------------------------------------------------------- > APBS -- Adaptive Poisson-Boltzmann Solver > Version 0.5.1 > > Nathan A. Baker (ba...@bi...) [... various lines of text ...] > ---------------------------------------------------------------------- > 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 Jul 17 2007 at 10:25:13 > apbsrun) Warning: possible problem while running APBS: ********************** > ERROR -- CALLED WITH TOO MANY ARGUMENTS! > > > ---------------------------------------------------------------------- > This driver program calculates electrostatic potentials, energies, > and forces using both multigrid and finite element methods. > It is invoked as: > > apbs [options] apbs.in > > where apbs.in is a formatted input file and [options] are: > > --output-file=<name> Enables output logging to the path > listed in <name>. Uses flat-file > format is --output-format is not used. > --output-format=<type> Specifies format for logging. Options > for type are either "xml" or "flat". > --help Display this help information. > --version Display the current APBS version. > ---------------------------------------------------------------------- > > ****************** > apbsrun) Cannot access output file C:/Documents and Settings/lfsqak/My Documents > /temp/apbs.42662/pot.dx The VMD pugin itself gives the message: APBSRun: output files missing or unreadable. I am using VMD 1.8.6 with Windows XP. I would be greatful for any help. Many thanks Andreas |
From: Nathan B. <ba...@cc...> - 2007-08-30 12:32:37
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Hello -- This might be caused by saving the APBS input and/or PQR files in a directory with spaces in its pathname. Can you try saving these files to another directory (without spaces in the path; e.g., C:/temp/) and see if that fixes the problem? Thanks, Nathan On 8/29/07, Andreas Kukol <a....@he...> wrote: > Hi everybody, > > When I try out the same example as in the tutorial 'How do I visualize > the electrostatic potential around by biomolecule' using the 1MYK pdb > file I get the following error messages (see ****): > > > apbsrun) Running job mode=normal > > apbsrun) dir is C:/Documents and Settings/lfsqak/My Documents/temp/apbs.42662 > > apbsrun) using VMD radii > > apbsrun) using pqrplugin for C:/Documents and Settings/lfsqak/My Documents/temp/ > > apbs.42662/test.pqr > > Info) Opened coordinate file C:/Documents and Settings/lfsqak/My Documents/temp/ > > apbs.42662/test.pqr for writing. > > apbsrun) Output files pot > > Info) Finished with coordinate file C:/Documents and Settings/lfsqak/My Document > > s/temp/apbs.42662/test.pqr. > > ---------------------------------------------------------------------- > > APBS -- Adaptive Poisson-Boltzmann Solver > > Version 0.5.1 > > > > Nathan A. Baker (ba...@bi...) > [... various lines of text ...] > > ---------------------------------------------------------------------- > > 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 Jul 17 2007 at 10:25:13 > > apbsrun) Warning: possible problem while running APBS: > ********************** > > ERROR -- CALLED WITH TOO MANY ARGUMENTS! > > > > > > ---------------------------------------------------------------------- > > This driver program calculates electrostatic potentials, energies, > > and forces using both multigrid and finite element methods. > > It is invoked as: > > > > apbs [options] apbs.in > > > > where apbs.in is a formatted input file and [options] are: > > > > --output-file=<name> Enables output logging to the path > > listed in <name>. Uses flat-file > > format is --output-format is not used. > > --output-format=<type> Specifies format for logging. Options > > for type are either "xml" or "flat". > > --help Display this help information. > > --version Display the current APBS version. > > ---------------------------------------------------------------------- > > > > > ****************** > > apbsrun) Cannot access output file C:/Documents and Settings/lfsqak/My Documents > > /temp/apbs.42662/pot.dx > > The VMD pugin itself gives the message: APBSRun: output files missing or > unreadable. > > I am using VMD 1.8.6 with Windows XP. > > I would be greatful for any help. > > Many thanks > Andreas > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. > Still grepping through log files to find problems? Stop. > Now Search log events and configuration files using AJAX and a browser. > Download your FREE copy of Splunk now >> http://get.splunk.com/ > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users > -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |