ADL: The question about ligand preparetation

Biao Ma jacky.b.ma at gmail.com
Thu Aug 7 00:04:58 PDT 2014


Hi, all

Now, I have some questions when prepare ligands before perform virtual
screening use vina.
Q1:
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
--gen3D"

Here, I want to known whether I have to process the output PDBQT use
prepare_ligand4.py?

Q2:
I read some scripts for prepare ligand,
some one use "prepare_ligand4.py -l ligand -o out.pdbqt -A checkhydrogens"
 and
some one use "prepare_ligand4.py -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.
Jacky


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