Hello there.
I am dealing with the extraction of ligand coordinates (in PDB) from
the typical autodock output file (DLG). Using simple shell routine I
can do it in just few steps:
# convert DLG to PDBQT
grep '^DOCKED' test.dlg | cut -c9- > ${output}/test.pdbqt
# convert PDBQT to PDB
cut -c-66 ${output}/test.pdbqt > ${output}/test.pdb
# take pdb of the receptor protein (used for this docking!) and add
it to the ligand ensemble
cat receptor.pdb ${output}/test.pdb | grep -v '^END ' | grep -v
'^END$' > ${output}/complex_test.pdb
The problem of this routine is in the last step when I add the
receptor pdb to the ligand ensemble - it actually creates multi-model
pdb (nmr like format) where the receptor is present only in the first
model (and the ligands in the rest). So I can not examine in PyMol
protein-ligand interactions (only even if I use split_states to
separate all models).
Could someone suggest a modification of my shell routine capable of
adding a receptor.pdb to each of the ligand models (thus obtaining
complex in proper multi-model format similar to NMR structure or
molecular dynamics trajectory)?
Thanks!!
J.
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