[Chimera-users] problem with pdb file saved from chimera-autodock vina analysis

Amol Ghodke a.ghodke at uq.edu.au
Tue Mar 2 21:04:42 PST 2021

First of all thank you so much for making such a wonderful tool and sharing it freely with scientific community.
I have been using chimera for sometime now and performed docking analysis using autodock vina.
I recently come across a problem.
After exporting pdb file with desired docking pose, I tried to run protein ligand interaction analysis on PLIP<https://plip-tool.biotec.tu-dresden.de/plip-web/plip/index> server. But ligand in my file does not get recognised for analysis.

I opened pdb file in a text editor and upon looking care fully I see chimera saves receptor and ligand as separate model like this
ATOM 7453 HD2 PRO A 462 15.986 11.983 20.450 1.00 0.00 H
ATOM 7454 HD3 PRO A 462 16.532 10.334 20.885 1.00 0.00 H
HETATM 1 S1 CGT A 1 9.051 5.106 43.099 1.00 0.00 S
HETATM 2 C6 CGT A 1 8.150 3.680 42.370 1.00 0.00 C

After comparing it with the pdb file from pbd database I removed “ENDMDL” and “MODEL 2” and re-ran the PLIP analysis. This time it works but PLIP also mentions that –
[cid:image001.png at 01D7103D.5D0AB030]
Analysis went well but the .pse file that I get from PLIP server does not allow me to show ligand in stick format in Pymol software.
I suspect this is due to the original pdb file format. I also noticed that pdb file when opened in pymol shows ligand and receptor as different states which is not correct (if I am right).
I have attached both original pdb file that I saved from Chimera-autodock vina and pse file from PLIP analysis.
May I request to help me resolve this issue?
Please let me know if you need any further information or clarification.

Thanks for your time and support

Dr Amol Bharat Ghodke | Post-Doctoral Research Fellow

Queensland Alliance for Agriculture and Food Innovation
Level 3, Queensland Bioscience Precinct [#80]
Room 3.318, 306 Carmody Rd, St Lucia
The University of Queensland
St Lucia, Brisbane Qld 4072, AU
E. a.ghodke at uq.edu.au<mailto:a.ghodke at uq.edu.au>

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