If you have a small number of files (for example in PDB format) you can convert them into smiles using various online software (Ex. cactus). If you have a large number of files to be converted into smiles, you can use other dedicated programs such as open babel. If use a particular database such as drugbank or Zinc, you can directly download structures in smiles format.
Thanks for the highlight. OpenBabel has its own limitations. it's important to perform thorough validation of the docking results obtained using Open Babel, potentially by comparing them with experimental data or other computational methods.
Hi, thanks for your video, that is great! And can you please let me know how to prepare SMILES files? thanks
If you have a small number of files (for example in PDB format) you can convert them into smiles using various online software (Ex. cactus). If you have a large number of files to be converted into smiles, you can use other dedicated programs such as open babel. If use a particular database such as drugbank or Zinc, you can directly download structures in smiles format.
OpenBabel adds all charges in the PDBQT file as '0.000'. This leads to inaccurate docking results. DON'T USE IN DOCKING THESE FILES
Thanks for the highlight. OpenBabel has its own limitations. it's important to perform thorough validation of the docking results obtained using Open Babel, potentially by comparing them with experimental data or other computational methods.
no its not true
The same command working for windows 7 also?
Is it possible for you to perform this feature on Windows? Thanks
If you have cygwin terminal, there is a method you can try.
OpenBabel adds all charges in the PDBQT file as '0.000'. This leads to inaccurate docking results. DON'T USE IN DOCKING THESE FILES