The following shows up when I try to run the APBS
tutorial (we're still in the set-up stage):
Parsing input file apbs-graphics.in...
Parsed input file.
Got PQR paths for 3 molecules
Reading PQR-format atom data from bx6_7_lig_apbs.pqr.
Vio_ctor2: some error occurred.
Vio_ctor: Vio_ctor2() failed.
Problem opening virtual socket bx6_7_lig_apbs.pqr!
Error reading molecules!
Yahoo! Mail - PC Magazine Editors' Choice 2005
Hi Caroline -
It looks like APBS is having problems finding the PQR file - this is
probably one of two things:
* Make sure the file is saved as bx6_7_lig_apbs.pqr and in the same
directory as the apbs-graphics.in file
* You'll need to call APBS from this directory - calling from a
different directory will only work if the input file has the full path
to the PQR file. For instance,
should work, since bx6_7_lig_apbs.pqr is in the current working
directory. Calling apbs from another directory (like the bin directory
where the executable is placed)
will not work, since APBS will look for bx6_7_lig_apbs.pqr in the
current directory, which is not where the file is. You could get
around this by always specifying the absolute path to the PQR file in
the input file, but this probably makes things a little less flexible
(especially if you ever rename directories).
Hopefully this helps!
Caroline Osborne wrote:
> The following shows up when I try to run the APBS
> tutorial (we're still in the set-up stage):
> Parsing input file apbs-graphics.in...
> Parsed input file.
> Got PQR paths for 3 molecules
> Reading PQR-format atom data from bx6_7_lig_apbs.pqr.
> Vio_ctor2: some error occurred.
> Vio_ctor: Vio_ctor2() failed.
> Problem opening virtual socket bx6_7_lig_apbs.pqr!
> Error reading molecules!
> Any suggestions?
> Yahoo! Mail - PC Magazine Editors' Choice 2005
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