[gmx-users] suggest small revision to genbox

David Mobley dmobley at gmail.com
Fri May 11 23:27:23 CEST 2007


I'm trying to write some wrappers to set up a project using standard
gromacs tools. Anyway, it looks to me like genbox is not handling its
path names correctly. In particular, here's what I did:

- Make temporary directory in which to run genbox
- Move to temporary directory, run genbox (reading input files from
permanent directory; writing input files to permanent directory)
- Change back to starting directory; delete temporary directory

When I do this, I get a blank output topology file in my permanent directory.

It appears what's going on is that the file temp.top is written into
my temporary directory, but never moved into the permanent directory;
I suspect genbox is not handling the absolute/relative path issue
correctly here?

I can work around, but this is just a bit annoying -- when I script
it, I end up with a bunch of "#temp.top.1#" etc files in my working
directory if I use editconf in the normal way, which is why I was
using the temporary directory thing to begin with.


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