I want to use the Prodigy web server for getting binding affinity for the protein-ligand complex. but unfortunately, I have got this error"Error during parsing the input structure: (1.pdb - Ligand LIG not found in chain A of the input data.). I checked my pdb file but I could not find any problem and ligand has existed in chain A. what is my problem and how can I solve it? I will send my pdb file in this post.
thanks for helping me
1.pdb (378.6 KB)
First of all use the ligand version of PRODIGY.
And I would try giving a different chainID to your ligand to distinguish it from your protein.
I did this but I got the same error.
Looking at your PDB file the atom names in the ligand are not unique. Most likely causing a problem.
The problem seems to come from the lower case naming of your ligand.
LIG made it work:
thanks for your helping me
I changed the name of lig to LIG but I got the error again" Error during parsing the input structure: (1-3.pdb - Selected chain not present in provided structure: B)". could you please send me the PDB file which you corrected to check it with mine. thanks
Here is the corrected PDB I used.
1.pdb (326.8 KB)
thanks so much for paying attention to my problem