Hi Georgios --
I am a newcomer in this field and the use of APBS. I am trying to
produce
an electrostatic potential map for a protein surface and I am using
Windows XP. Although I have installed succesfully Pymol v0.99, APBS
v0.4.0
and the M.Lerner's plug-in,following Lerner's instructions, I can
load my
pdb file, I can generate the .pqr and .in files, but the programme
doesn't
generate the .dx file resulting to the message:
ObjectMapLoadDxFile-Error:Unable to load file!
This typically means (1) something is misconfigured in the APBS/PyMOL
setup such as spaces in the path to the APBS binary, etc., or (2)
something went wrong with the APBS calculation. To rule out the
second case, can you locate the APBS input file and PQR file you're
using with these calculations and send them along for debugging
purposes?
Is there any incopatibility or lack of commands or scripts that
elude me?
I tried the VMD v1.8.5 and v1.8.4 to visualize the electrostatic
potential
following the instructions from the tutorial, but the procedure is
stopped
at the same stage... Cannot load the .dx file because it doesn't
exist..
This definitely sounds like a probably with the calculation -- the
relevant APBS input and PQR files should help us track this down.
Thanks,
Nathan
I searched the APBS,Pymol and VMD forums but I couldn't find a
solution.
Please Help me!
Villias Georgios
Bioinformatics Postgraduate student
University of Athens - Greece
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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/
