Hi Muniba, I would like to follow on a previous question I have posted with regards to adding a new atom type in AutoDock Vina. My ligand contains Boron atom (B), which is not included by default in the \’AD4_parameters.dat\’ file.
I have added a line for B atom with all atom references but it still gives me an error
\"ATOM syntax incorrect: \"B\" is not a valid AutoDock type\".
From my reading in AutoDock 4, we shall add a line \’Parameter_file modified_AD4_parameters.dat\’ in AutoDock and AutoGrid which don\’t exist in Vina. I would appreciate your help. Thanks in advance
User Changed status to publish November 23, 2024
Perform force field optimization of your ligand in Vina. Vina uses amber force field by default, try using UFF.
User Changed status to publish November 23, 2024