As a docking post-processing tool, the main purpose of Fast Amber Rescoring server is to rescore docked poses to identify the near native binding pose of a ligand. Based on our benchmark, it can be confirmed that several MM/PB(GB)SA calculation procedures have distinct advantage over the docking scoring function (Glide SP) on pose ranking for PPI-inhibitor systems.
Fast Amber Rescoring server provides 7 different MM/PB(GB)SA procedures (i.e., PB1, PB3, PB4, GB1, GB2, GB5, GB6) to calculate binding free energy of protein-ligand. The numbers followed by PB and GB are the type of Poisson-Boltzmann calculation and generalized Born calculation, respectively. The parameters of each calculation procedure are the same as the ones of workflow for automated MM-PBSA & MM-GBSA calculations (WAMM) in AmberTools17 (see AmberTools17 manual page 724-725 for detailed information).
If the download link of result file is not generated successfully, that means fatal error occurred during the calculation and the workflow was interrupted. You should check input files according to the instructions. If result.zip file can be downloaded, but there are only log files (without csv and pdf files), that means the final MM/PB(GB)SA calculation is not completed successfully. You can find the potential reasons for failure in log files.
No. The result file of each finished project on Fast Amber Rescoring server can be downloaded directly by anyone. In order to control the size of result file and protect the users’ data, only the final binding free energy data files and several log files are available to download.
It depends on the size of protein-ligand complex and the selection of calculation procedure. Obviously, it will take more time to process the bigger system with all procedure than the smaller one with single procedure.
The result formats of the toDock and AutoDock Vina are dlg and pdbqt which are unacceptable for Fast Amber Rescoring server. Thus, format conversion is needed before submitting a job. Here, we provide two scripts (pdbqt2mol2.py and run_pdbqt2mol2.sh) that can be used to convert dlg and pdbqt format to mol2 based on Pybel. These scripts come without warranty of any kind. Use them at your own risk.