Hello, I am getting the error while converting a ligand sdf file to pdbqt format. How do I solve it? I got the error after I ran the following script
mk_prepare_ligand.py -i L19.sdf -o ligand.pdbqt
TIA
Rabeya
Rabeya, have you identified the atom at the 27th position? I think it contained an atom with a valency of more than 4. Delete atom no. 27. It will be a simple way out.
Have you energy mnimized your ligand molecule??
If not, do minimize it, this will solve the purpose.
Use Avodagro for the same
Regards
You appear to have a neutral nitrogen atom bonding to four other atoms - This is not possible: look at the molecule in detail, especially atom #27 and the atoms surrounding it: if the nitrogen participates in four bonds, it needs to carry a positive charge. If there are fewer atoms within bonding distance, you may have to correct the bond orders of these bonds.
Just deleting the offending atom is no solution - it will leave the atoms bonded to it with unsatisfied valences. Also, energy minimisation is no solution for a faulty covalent structure. Make sure you have the chemistry correct before doing anything else.
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