I used the Discovery studio for molecular docking analysis and obtained the best pose by flexible docking. I need to further analyze this result using PYMOL or Ligplot, but when I saved the result (receptor with ligand) in PDB format and open in above-mentioned, software, there was the only receptor. How do save both ligand and receptor?
Dear Venkataraghavan Ragunathan
I used discovery studio for docking and I saved ligand and receptor complex in pdb format by discovery studio. Moreover, when I open it in discovery studio, I got both receptor and ligand, but when I open the same file in PyMOL or Ligplot, there was only the receptor.
D.P. Nagahawatta : Please try the following in PyMOL:
1. Open the PDB file in PyMOL.
2. In the second line of the right-hand panel that lists the title of your file, click on "S" (Show). A menu will open. Move down to the heading "organic". A side-window will appear with choices such as "lines, sticks, spheres". Select the rendering you want from these three choices. The ligand should then appear.
Dear Rudy J Richardson , I tried but didn't work. I think the problem is in discovery studio. I need to know is there any specific way to save my docked file for use in other software.
D.P. Nagahawatta : Are you able to see both the receptor and ligand in PyMOL if you download a receptor-ligand complex in PDB format from the PDB? This would verify that PyMOL is working correctly for you. Please also try viewing the same downloaded PDB file in Discovery Studio and then save the file from Discovery Studio in PDB format, giving it a new name. Then open the new file in PyMOL. This would check the save file procedure in Discovery Studio.
Rudy J Richardson I followed this method several times to save my file in PDB format. When I open this file in Discovery studio, both receptor, and ligand had appeared, but in PyMOL only the receptor appeared.
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