Sdf to pdbqt converter
Hello, my name is Matthew Lovelace, I am a highschooler and for one of my classes I am working on a project that uses Autodock Vina. So to run Autodock Vina I need to make sure the files I am using are in pdbqt format so it is required I convert them from their original formats. One set of files I am using is in sdf format so I first must convert them to pdb format using openbabel and then to pdbqt format using Autodock Tools. When I run the command:
It gives me a file in pdb format which I then convert into pdbqt format but when I try to run Autodock Vina using the following command:
I get the following error:
Iâm assuming the error is with the sdf to pdb conversion since Iâve used Autodock Tools before to convert pdb files and I haven't had any problems.
Am I using the wrong command to convert my sdf file to pdb, or is there something Iâm just not doing correctly?