I am conducting a molecular docking study using peptides as ligands. I successfully ran the docking process using autodock vina, and when I viewed it using Discovery Studio, I realized that the ligand have missing bonds. I retracked my process and found out that the pdbqt file of my ligand is the problem. Here is a screenshot of my pdbqt file of my peptide, IF in DS. Attached also is the pdbqt file of my peptide.
Please help me on what to do.
Increase the threshold of the bond length. Make it longer manually.
@Jhashanat Adhikari how do I do that? Do i need to draw the peptide manually? I used the sdf file by converting the peptide sequence to a SMILES sequence then downloaded the sdf file frok pubchem. I used this file to generate the 3d model in Avogadro and autooptimize it.
Try to convert the sdf file to pdb file in chimera and then to pdbqt through openbabel....... Then you can visualize the structure for any breaks.....
This happens due to issues in the CONNECT part in the pdb file.
Jack Dela Cruz Is it possible to share the file..... Ill look into it
Regards
Jobin Thomas Hello. After many youtube tutorials, I think I found the answer. Yes, I built the structure using chimera. Then minimized the structure, following the default settings, then saved it as PDB. I opened it via the autodock tools (for the choose torsion option), then saved it as PDBQT. Finally, the structure is now complete.
Thank you!
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