Re: [PyMOL] [EXTERNAL] Protein-ligand multi-model pdb extracted from docking

[Mooers, Blaine H.M. (HSC)]

Hi Jeff,

I would se the pdb file 1nmr as a template to reformat your file accordingly: 
fetch 1nmr, type=pdb.
Open it with a text editor
You will see the that END is used only once, at the every bottom of the file 
after the last model.
This is why you are not seeing multiple models  with all_states.

You need to end the protein model with TER and then ENDMDL and start the ligand 
with 'MODEL        2'   

TER    1291      VAL A  85                                                      
ENDMDL                                                                          
MODEL        2   

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

________________________________________
From: Jeff Saxon [jmsstarli...@gmail.com]
Sent: Thursday, October 15, 2020 2:34 AM
To: pymol-users
Subject: [EXTERNAL] [PyMOL] Protein-ligand multi-model pdb extracted from 
docking

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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