[gmx-users] suggest small revision to genbox

bharat v. adkar bharat at sscu.iisc.ernet.in
Sat May 12 08:35:44 CEST 2007

genbox works fine for me. i use 3.3.1 version. it works fine with and 
without script.

but i don't understand how will u get rid of backup files in the permanent 
directory from whatever u have mentioned, because gromacs creates the 
output topology in the same location where it reads the input topology 
from. so temperory directory thing will work only if u make an link of top 
file from permanent directory and use this linked version as input, then 
move the new top from temp to permanent directory.


On Fri, 11 May 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.
> Thanks,
> David
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