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Browse QuestionsCategory: Questionsaddition-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

2 Answers
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 Faiza Staff replied 3 years ago

At 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.