[gmx-users] suggest small revision to genbox

[David van der Spoel]

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.
________________________________________________________________________
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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