ADL: The question about ligand preparetation

Biao Ma at
Thu Aug 7 00:04:58 PDT 2014

Hi, all

Now, I have some questions when prepare ligands before perform virtual
screening use vina.
I have one SDF file that contain multiple ligand molecule,  I converts the
SDF file to multiple PDBQT file use Open Babel (version: 2.3.2).
the command is :" babel <my sdf file> -f 1 -l 10 -opdbqt output.pdbqt -m

Here, I want to known whether I have to process the output PDBQT use

I read some scripts for prepare ligand,
some one use " -l ligand -o out.pdbqt -A checkhydrogens"
some one use " -C -l ligand -o outpdbqt".

which one is correct?
Is there a big effect of docking result when add charge or not add charge
in ligand?

Thanks a lot.

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