I have a lot of proteins and compounds to analyzed together. I do the ligand preparation add all hydrogens, add charges gasteiger, but some compunds disappear when I select the option "merge no polar". Why is this happened?, is a software problem or is due to the compound chemistry. How can I fixed it
Abdeen Tunde Ogunlana
My solution might sound weird but this would save you a lot of stress: You do not need to "merge nonpolar". If your ligand structure is in .pdb format; import the structure into the AutoDock4.2 tools (immediately you load your ligand, Gasteiger charges and the appropriate ff parameters are added by default. Thus, no need to add anything to the structure) Go to ligand > Output > save as .pdbqt
I hope this helps
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