Can anyone help me on this please?
Once the protein is prepared, when I open the ligand and try to do the torsion tree part, I get an alert box saying that I must select a ligand first. I can't understand why this happens because I already have the molecule I want selected in the left options of the dashboard. What am I missing?
Thank you!
In MGL tools you always open ligand through Ligand>input>open file, if already present in work space, if u need to prepare ligand, if it ask to select ligand first, then you goto Ligand>Input>Choose option, and under choose, you select your ligand and prepare you molecules.
you can use prepared molecule of your ligand here, hop it will work now.
ya, i hop, u remove water molecules and try it. or u draw molecule again, In the ligand some coordinates problem found.
please look your ligand file. when atomic coordination is not properly defined then AutoDock give this error.
Assign the atomic charges and optimize geometry using gaussian software. Then it will work
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