The Molecular Graphics Laboratory Forum

Hi all,

I know Vina was developed with the philosophy of requiring the least amount of parameter input from users, so I am not surprised there is no readily apparent way to add new atom types to Autodock Vina. I am wondering, however, if the functionality is there, just hidden.

I have researched this topic a bit and found how to add atom types to Autodock 4 at the following link:
http://autodock.scripps.edu/faqs-help/f ... autodock-4

The procedure for AD4 involves writing a new atom parameter file to which your atom of interest is added, then calling this parameter file in your .gpf and .dpf (grid parameter file and docking parameter file). Since Vina has done away with .gpf and .dpf files, this solution will clearly not work.

Does anyone know any methods that can be implemented in Vina?

Thanks,
Seth

I second this request. Vina does a way better job with docking for many of my structures, but the lack of atom profiles such as arsenic and copper make automated docking of large datasets impossible to perform.

New atom types can not currently be added by non-programmers. I hope you can still screen most of your library.

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Please do not email or PM me with questions. Vina.scripps.edu/questions.html explains where to find help.

I want to make clear that, in no way, my post was meant as a complaint or anything. I know how users sometimes can come across as a bunch of complainers with a huge sense of entitlement, especially when the software is freely distributed.

You people at Scripps make great software and give it all freely away for the progress of science, and I really, really appreciate that. I just want you to know, that if you ever have plans to expand upon AutoDock and AD Vina, I and other users would like to see some method of easy atom parameter setup implementation. It would make sense from an end-user point of view, especially with freely available ligand data sets, such as the NCI/NIH Diversity Set.

For now, I will just replace the atoms with closest analogues (arsenic with phosphorus, but I still have to come up with something for copper and palladium) and run the docking with Vina. I can always add the atom parameters to AutoDock 4, do the docking again, and compare the results.

Thanks, our work is actually taxpayer-funded. We recently proposed something like what you and others are suggesting, but more general, to the NIH funding agency: arbitrary user-supplied scoring functions and atom types for Vina, shareable like spreadsheets. (If you have any questions about this, please contact Prof. Olson, as he's the PI on the NIH proposal)

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Please do not email or PM me with questions. Vina.scripps.edu/questions.html explains where to find help.