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Running AutoGrid and AutoDock

MD Mycal Dutta
MN Mohammad Nezam
SC Subrata Chowdhury
AR Ahmed Rakib
AP Arkajyoti Paul
SS Saad Ahmed Sami
MU Md. Zia Uddin
MR Md. Sohel Rana
SH Shahadat Hossain
YE Yunus Effendi
RI Rinaldi Idroes
TT Trina Tallei
AA Ali M. Alqahtani
TE Talha Bin Emran
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After setting up the GridBox, the AutoGrid file was saved. When in the “Grid” menu, select the “Output” and “Save GPF” sub-menu. The file saves in.gpf format. Meanwhile, the AutoDock file saving procedure is to choose the “Docking” menu and select “Lamarckian GA” in the “Output” menu. The file saves in.dpf format. The AutoGrid and AutoDock programs was run through a command prompt directed to the folder to be docked using the command: autogrid4 -p control.gpf -l control.glg. After the AutoGrid calculation was completed successfully, AutoDock was run using the command: autodock4 -p control.dpf -l control.dlg. The results of the docking calculations are obtained in a notepad file format, reporting the values for binding energy and the estimated inhibition constant.

Copyright and License information:  ©2021 Dutta, Nezam, Chowdhury, Rakib, Paul, Sami, Uddin, Rana, Hossain, Effendi, Idroes, Tallei, Alqahtani and Emran.
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