I am running an up-to-date installation of Buster on my Linux platform
and have run into a strange problem with a bash script.
I have a number of ligand protein docking applications which involve
ligand sets docking on a protein and am using Autodock with the the
Racoon file editor (https://autodock.scripps.edu/).
I have written a bash script which runs each set of ligand dockings:
#!/bin/sh
for d in $(cat ligand.list)
do
cd "${d}_apo-3k9b"
echo "${d}apo-3k9b"
echo "${d}apo-3k9b.dpf"
/home/comp/Apps/Autodock/autodock4 -p "${d}apo-3k9b.dpf" -l
"${d}apo-3k9b.dlg"
cd ..
done
The script has run successfully for several sets of ligands, but now
there is a problem:
comp@AbNormal:~/Apps/Models/1-PhosphorusLigands/Acetylcholinesterases/3K9B/Results$
./Run.ligand.list.sh
./Run.ligand.list.sh: line 3: cd: $'Acetylcholine\r_apo-3k9b': No such
file or directory
apo-3k9boline
apo-3k9b.dpfe
apo-3k9b.dpfpps/Autodock/autodock4: can't find or open parameter file
Acetylcholine
/home/comp/Apps/Autodock/autodock4: Unsuccessful Completion.
The problem is in the first 'cd' command in the do loop which is looking
for 'Acetylcholine_apo-3k9b', but is finding 'Acetylcholine\r_apo-3k9b',
and consequently, does not change in to the directory
'Acetylcholine_apo-3k9b'!
The only difference from the script that ran the previous successful
dockings, the '\r', is that I edited the script for the current use by
changing the name of the protein, in this case 'apo-3k9b'. I used Jedit
to edit the script and have no idea as to the source of the '\r' as
Jedit is using the Unix(\n) line separator.
Google has been of no help is solving the problem.
Any suggestions will be much appreciated.
Thanks in advance.
--
Stephen P. Molnar, Ph.D. Life is a fuzzy set
http://www.Molecular-Modeling.net Multivariate and stochastic
614.312.7528 (c)
Skype: smolnar1
