Problems with sdf to pdb file conversion
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6.7 years ago

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:

babel /Users/mattlovelace/Desktop/SDFformat/structures_nutraceutical/DB00114.sdf DB00114.pdb 

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:

./autodock_vina_1_1_2_mac/bin/vina --receptor protein.pdbqt --ligand DB00114.pdbqt --center_x 11 --center_y 90.5 --center_z 57.5 --size_x 22 --size_y 24 --size_z 28

I get the following error:

Parse error on line 22 in file "DB00114.pdbqt": Unknown or inappropriate tag

I’m assuming the error is with the sdf to pdb conversion since I’ve 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 I’m just not doing correctly?

Thanks in advance for any suggestions,


pdb sdf • 4.4k views

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