When I used autodock to dock a protein and a molecular, a problem occured. The structure of small molecular is Fig A, but when I opened in autodock, it changed like Fig B. I don't know what happened. When I opened the Receptor protein in autodock and Select From String, a problem like Fig C. I don't know what's the reason. Can anybody help?
Dear friend,
Its just a graphical issue. After adding hydrogen to the ligand this weird connections will disappear.First you must remove the unusual hydrogen connection in figure A then add hydrogen to the ligand. If your problem still remained add hydrogen to the ligand using other programs such as chimera then load your ligand and continue the process without adding hydrogen.
2-What is your purpose of selecting HOH molecules? to remove them?If yes, I suggest opening pdb file using text editors (e.g.context) and removing this molecules manually. Anyway there is no HOH* residue in the pdb files (remove * in selection).
finally I have a simple instruction file about docking process.
Best,
HHA
Dear，Hamed Haghshenas
Thank you very much for you help! And I have a new problem when I operate to this step: ligand-torsion tree-detect root, the window display this result(Fig), I don't know pyton, so can you tell me what's the reason about this result,and what I should do?
Best wishes,
Q, W
As you mentioned program failed to detect root for your ligand.Its a general problem report. First check your ligand pdb file, search for abnormal atom types and rerun auto-dock tools if your problem still remained send me your files I will consider it.
best
Sorry compute kollman means add kollman charges. As I said before its a simple and abbreviated instruction. Anyway I prepared and sent docking result.please check your inbox
regards,
HHA
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