To obtain the same result with the newer command cpptraj
(Amber 14) add the keyword multi at the end of the last line. The
example above assumes that the production run sys5.mdcrd is in
the current directory and that the equilibrated trajectory spans
frame numbers from 3001 to 10,000. The increment is equal to
1, hence all 7000 frames will be extracted. Also, the receptor in the
example above has 290 residues. You should adjust these numbers
to your specific case.
The second step adjusts the file numbering format to the input
requirements of the kclust program. The numbers should have
leading zeros and be written with five characters. This is done by
the script below:#! /bin/csh
set DIR=’PDB’
set ff = ‘ls -1 ${DIR}/*.pdb.* | head -1‘
set fnam = $ff:r
set numfil = ‘ls -1 ${DIR}/*.pdb.???? | wc -l‘
if( $numfil != 0)then
foreach fnam (${DIR}/*.pdb.????)
set fr=$fnam:r
set fnum=$fnam:e
mv $fnam $fr.0$fnum
echo $fnam $fr.0$fnum
end
endif
set numfil = ‘ls -1 ${DIR}/*.pdb.??? | wc -l‘
if( $numfil != 0)then
foreach fnam (${DIR}/*.pdb.???)
set fr=$fnam:r
set fnum=$fnam:e
mv $fnam $fr.00$fnum
echo $fnam $fr.00$fnum
end
endif
set numfil = ‘ls -1 ${DIR}/*.pdb.?? | wc -l‘
if( $numfil != 0)then
foreach fnam (${DIR}/*.pdb.??)
set fr=$fnam:r
set fnum=$fnam:e
mv $fnam $fr.000$fnum
echo $fnam $fr.000$fnum
end
endif
set numfil = ‘ls -1 ${DIR}/*.pdb.? | wc -l‘158 Gre ́gory Menchon et al.