open babel: how to create multiple output files (split the input)?

Question

I have a .pdb file containing multiple conformers of the same molecule. Now I want to convert each of those conformers to a separate .xyz file. According to the open babel help, this could be done with the -m option.

-m Produces multiple output files, to allow:
   Splitting: e.g.        babel infile.mol new.smi -m
    puts each molecule into new1.smi new2.smi etc
   Batch conversion: e.g. babel *.mol -osmi -m
    converts each input file to a .smi file

But this converts only the first geometry and then stops:

babel -ipdb confs.pdb -oxyz test.xyz -m
  1 molecule converted
  14 audit log messages

(Tested open babel 2.3.2 on Ubuntu and OSX)

Any suggestion how to fix that or which program to use instead?

Ok, it seems to work with .sdf, but not with .pdb so far. – tmartin Apr 16 '15 at 13:35 — tmartin, Apr 16 '15 at 13:35

score 0 · Answer 1 · edited Aug 25 '20 at 15:55

Split your pdb file using this linux command:

grep -n 'MODEL\|ENDMDL' models.pdb | cut -d: -f 1 | \
 awk '{if(NR%2) printf "sed -n %d,",$1+1; else printf "%dp models.pdb > model_%03d.pdb\n", $1-1,NR/2;}' |  bash -sf

Input file is models.pdb, and split file will be named as model_0001.pdb, model_0002.pdb...etc

More details here: https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Split_NMR-style_multiple_model_pdb_files_into_individual_models

open babel: how to create multiple output files (split the input)?

1 Answers1