[gmx-users] suggest small revision to genbox

David van der Spoel spoel at xray.bmc.uu.se
Sat May 12 11:13:00 CEST 2007

David Mobley wrote:
> All,
> 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.
Hi David,

plz submit a bugzilla with all input and scripts.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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