I performed molecular docking using auto dock tools, specific protein was docked with different ligands. During the preparation of ligand.pdbqt files, I should select the same number of active torsions for these ligands. When I open ligand.pdb file, the program tell me about the number of active torsions for this ligand which differ from one ligand to another. Actually, I fixed the number of active torsions for all ligands =4. I do not know if this right or not. Please, can any one help in this issue?
Thanks in advance.
Aliaa M. Radwan
Assalam o alaikum wa rahmatullahi wa barkatuhu
hope you doing well
As per your queries, In the AutoDock tool torsion no. sets by default. If you specified the torsional no. so you can identify rotatable bonds and choose torsion numbers then prepare ligands.
we alaikum Assalam wa rahmatullahi wa barkatuhu
Thank you Waseem Ahmad Ansari.
Hi
When you give the docking command to the desired software, you can specify how many rotations the ligands have and how many of the best rotations should be displayed at the end, this command is the same for all ligands. MOE software has this possibility. has the
It is your choice how many spins to have, of course, the more spins, the longer the calculations will take.
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