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
Why are you docking using Vina? If you have prepared your files using AD4, then perform docking with AD4 itself?
At what step are you getting this error? While preparing ligand or running vina?
Running vina.
I have prepared ligand and protein accordingly and prepared the conf.txt file as well
I have prepared my files using vina. (I dont even have AD4)
I only mentioned AD4 , because I could only find answers for my question for AD4 not Vina, that’s why I am looking for an answer for Vina (Adding new atom types in AutoDock Vina)