addition-of-atom-type-in-autodock-vina
bellag.oualid asked 3 years ago
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
Dr. Muniba Faiza Staff answered 3 years ago
Why are you docking using Vina? If you have prepared your files using AD4, then perform docking with AD4 itself?
bellag.oualid
replied 3 years ago 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)
Muniba FaizaAt what step are you getting this error? While preparing ligand or running vina?
bellag.oualid
replied 3 years ago Running vina.
I have prepared ligand and protein accordingly and prepared the conf.txt file as well
Dr. Muniba Faiza Staff answered 3 years ago
Perform force field optimization of your ligand in Vina. Vina uses amber force field by default, try using UFF.
