"Error Converting File!" issue

[Ziziphus]

Hi community!
I am using Webvina for tool-like receptor research. However an "Error Converting File!" issue occurred when uploading proteins .
This issue will happen when:
1 uploading .pdb file downloaded from rcsb with option "Add hydrogen atoms at PH (7.4)" clicked
2 uploading .pqr file generated with PDB2PQR, no matter if "Add hydrogen atoms at PH (7.4)" clicked
3 uploading .pdb file manually deleted ligands and added hydrogen with pymol, no matter if "Add hydrogen atoms at PH (7.4)" clicked

This issue will NOT happen when uploading .pdb file downloaded from rcsb WITHOUT option "Add hydrogen atoms at PH (7.4)" clicked, but I am not sure if its docking result reasonable.

Best regards!

screenshot:
https://s1.ax1x.com/2023/04/21/p9AHZWj.jpg

[Jacob Durrant]

Hi Ziziphus,

Thanks for reaching out about the issue you encountered while using Webina. I appreciate your interest in the tool.

It's difficult to diagnose the error without access to the specific files you're working with. But, I suspect the problem arises when the protein becomes too large for the browser to handle because of the addition of hydrogen atoms (which are likely critical for accurate docking).

One potential workaround could be to select only the amino acids within a certain distance, such as 15 angstroms, of the binding pocket and dock into this smaller version of the protein. This solution isn't exactly elegant, but I suspect it would bypass the error.

I hope this helps!

Take care,
Jacob

[Author]

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