Hi there,
I've got a text file with multiple conformations of a ligand that has been
docked to a protein using autodock, which I am trying to split into separate
pdb files in order to visualise in pymol/coot etc.
Previously I've used the script pasted below, but it is now falling over just
after it creates the pdb file with the error:
expr: syntax error
csplit: }: bad repetition count
./split_results.com: line 11: syntax error near unexpected token `('
./split_results.com: line 11: `foreach f ($outputname.[0-9][0-9][0-9])'
Can any of you wizzy programmers give me a hand with getting this to work
again? (it's on a mac just in the normal terminal)
Thanks,
Simon
The script:
#!
grep '^DOCKED' output.dlg | cut -c9- > my_docking.pdbqt
cut -c-66 my_docking.pdbqt > my_docking.pdb
# csh to split pdb files from autodock output.
# edit outputname.
#
set outputname=output
set a=`grep ENDMDL my_docking.pdb | wc -l`
set b=`expr $a - 2`
csplit -k -s -n 3 -f $outputname. my_docking.pdb '/^ENDMDL/+1' '{'$b'}'
foreach f ($outputname.[0-9][0-9][0-9])
mv $f $f.pdb
end
