After using autodock gpu , i can just see the poses , but in the .dlg file , i cannot see any binding energy value. So is it like autodock will covalently each and every molecule , but then isnt it specific in identifying or screening which molecule can covalently dock or not. In conventional docking , we usually screen on the basis of their docking scores/binding energy . But in this case , how do we identify this. I tried using the old version where only cpu is used. I reached the last stage , but when i use autodock.exe for docking , it takes a lot of time. Even after 12 hours its not getting ended. When i changed the energy evals from 1.2 million to 50000 , it happens instantly and the docking scores are in the range of -2 to -4 which are not good considering good docking scores to be above -5. What should i do to increase the speed , because cpu version is the only thing that is giving me docking binding scores.
After using autodock gpu , i can just see the poses , but in the .dlg file , i cannot see any binding energy value. So is it like autodock will covalently each and every molecule , but then isnt it specific in identifying or screening which molecule can covalently dock or not. In conventional docking , we usually screen on the basis of their docking scores/binding energy . But in this case , how do we identify this. I tried using the old version where only cpu is used. I reached the last stage , but when i use autodock.exe for docking , it takes a lot of time. Even after 12 hours its not getting ended. When i changed the energy evals from 1.2 million to 50000 , it happens instantly and the docking scores are in the range of -2 to -4 which are not good considering good docking scores to be above -5. What should i do to increase the speed , because cpu version is the only thing that is giving me docking binding scores.