I am trying to dock the SA receptor to avian influenza HA binding site using Autodock 4.2, following the protocol by Rizvi et al, 2013 (A simple click by click protocol to perform docking: AutoDock 4.2 made easy for non-bioinformaticians). When the docking is completed, the interaction file (complex.pdb) is retrieved by using Discovery Studio Visualizer. However, at this step, the file cannot be opened with an error "File must contain valid atoms to import as a PDB file". As I am very new in this field, can anyone please help me with this error?
Check the format of the receptor-ligand file. It should be in PDB format (Protein Data Bank) file.
Ahmed Adebayo Ishola Yes, the file is in PDB format
Dr Thirumal Kumar D Please find attached. Thanks!
Giang, You should try PyMol for visualization of your complex.pdb file.
Giang Nguyen Discovery studio was able to visualize it. Find the interaction attached
Dear Ahmed Adebayo Ishola ,
Thank you very much for your immediate reply. I have just found out that there is a mistake in the linux command from the protocol which is supposed to be typed in the cygwin-window in order to obtain the complex.pdb file (a space is between word is missing). Now the complex file can be opened. However, another error pops up.
After opening the file, I operate command "Script" --> "Ligand Interactions" --> "Show Ligand Binding Site Atoms" and the warning appears as "This script displays ligands and surrounding receptor atoms. Document does not contain both a receptor and a ligand molecule". Do you have any experience with this error? Did I still do something wrong before?
Thank you very much,
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