How to convert SDF to PDBQT for Molecular Docking | Autodock

[@radiantentity989]

Very useful, Thank you soo much, it saved soo much of my time.

[@BioinfoCopilot]

My pleasure! Thanks

[@naserianikambaine4934]

Thank you for this it really made easier for us. I am using Ionic liquid as a ligand, when I convert my file to pdbqt only the anion is remaining and cation is disappearing, could you please help with how to model ionic liquid as a ligand for docking? Thank you in advance

[@BioinfoCopilot]

Thank you. I think to deal with cations and anions you need to parameterize them and use them in the autodock. Use MGL tools to convert them to pdbqt.

[@naserianikambaine4934]

@@BioinfoCopilot Thank you for replying. I tried also in mgltools and also used the script form autodock still it does the same.

[@baoxuyennguyenle6435]

Thanks a lot sir. I have prepared my list of ligands (nearly 2000 molecules) following your instruction, however, I met this error:
*** Open Babel Error in Do
3D coordinate generation failed
1 molecule converted
1 molecule converted
1 molecule converted
......
and all 2D SDF files were not converted to 3D. Would you please to help?

[@BioinfoCopilot]

Check the output folder that out of 2000 how many were converted. Then analyze what’s wrong with the not converted ones. Do it manually one by one if the issue persists again and again.

[@keerthikeerthika375]

i was unexpected at this time. i have getting this command what i have to do it

[@BioinfoCopilot]

What kind of error did you get?

[@namalranaweera9623]

and there is a bash syntax error in this command
for i in *.sdf; obminimize -ff MMFF94 -n 1000 $i

[@BioinfoCopilot]

for i in *.sdf; obminimize -ff MMFF94 -n 1000 $i; done

[@volkzreyes1005]

for i in *.sdf; do obminimize -ff MMFF94 -n 1000 $i; done

[@juhidutta6121]

Thank you. It saved a lot of time. 😀

[@BioinfoCopilot]

My pleasure

[@sonuverma8139]

How make a single pdbqt file for all drugs?

[@BioinfoCopilot]

Paste all the pdbqt files in a text editor and save it. You can also weite a simple bash command to perform the task as well.

[@Chaloniper]

Thanks a lot Sir.its very helpful for me.

[@BioinfoCopilot]

My pleasure 😇

[@namalranaweera9623]

Thank you for the great content. It really helped.
One question, how can we get the molecular name in to the .pdbqt output file name?

[@BioinfoCopilot]

Use "${filename%.*}.pdbqt" to get the output file name.

[@namalranaweera9623]

@@BioinfoCopilot Great! Thank you!

[@fatimanaeem9067]

I have used your method but some of my ligands structures were distorted in the end. when converting the 2d to 3d coordinates openbabel was unable to perform the conversion function properly. These structures have given wrong results in vina. kindly make a video regarding the errors that may have arise in the procedure.

[@BioinfoCopilot]

Sure will do that. Thanks 😊. Could you please give the id of the molecules that you are converting: pubchem, drugbank or chembl ids