I wanted to prepare a protein at an alkaline pH for molecular docking as that is the pH I want to perform my in vitro assays in? I prepared my protein at the required pH through H++ server; subsequently when I tried generating the PDBQT structure from the PDB file error message appeared in ADT 4.2 stating: Error parsing in PDB in following line.
How shall I proceed for docking in such case?
First - look at the particular line of the pdb file referred to by the error message. You can look at a pdb file in a simple text editor, as it is an ascii text file. Make sure that there is not a trivial reason such as a missing atoms or residues, alternative conformation, post-translational modification, non-protein compound.
A quick way to clean up a problematic pdb is to model the theoretical sequence of your molecule, using the experimental structure as a template, e.g. using modeller.
Dear Debanjan,
ADT 4.2 performs in vacumm, hence in your docking study there is no sense of setting the pH of the medium. The charges that will be there in pdbqt, are generated based on the protein PDB file. Docking does not allow the change in pH thus modifications in charges of the protein. However, you can always add charges in simulation and can solvate the modified protein in the water box and then run your simulation.
Thanks a lot @Annemarie Honegger and @Ushasi Pramanik for the insights. I will read a bit more.
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