Hello –


That’s a very strange error.  Do you have permission to write to the directory in which you’re running APBS?



Nathan Baker
Pacific Northwest National Laboratory
Tel:  509-375-3997


From: dalit.shental@weizmann.ac.il [mailto:dalit.shental@weizmann.ac.il]
Sent: Wednesday, October 05, 2011 8:13 AM
To: apbs-users@googlegroups.com
Subject: [apbs-users] writing atompot


Hi All
I try to use the new flag atompot to get the potential on each atom. To this end I installed apbs1.3.
My input file works, I get the potential map but get an empty txt file for the atoms potentials.
The relevant commands in the input file are:
    write pot dx peptide
    write atompot flat AtomPotential

while apbs is running I get the line:
  Writing atom potentials to AtomPotential.txt
  Writing atom potentials to AtomPotential.txt
Vio_ctor2: Gethostbyname fail INET sock <> dueto <VIO_UNKNOWN_ERROR(24)>
Vio_ctor2: some error occurred.
Vio_ctor: Vio_ctor2() failed.
routines:  Problem opening virtual socket AtomPotential.txt

The file is empty of data, there are only few remarks lines:
# Data from APBS 1.3

Do you have any idea what I have been doing wrong?