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PostPosted: Thu Dec 29, 2016 7:16 pm 
Millimolar User
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Joined: Thu Dec 29, 2016 7:05 pm
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Hello everyone,

I am working on docking an organic molecule (to a protein) that has a boron atom. I am using autodock 4 and MGL tools 1.5.6. I have problem with executing autodock when I use the ligand molecule with boron.

Here is what I did
I downloaded the boron parameters from website ... meters.dat. I also looked the paper Tafi et al., Eur. J. Med. Chem 2005, 1134-1142 for boron parameters. Following the instructions from the Autodock website, I created a grid by choosing the ligand for atom types. In the gpf and dpf file, I chose
parameter file “AD4_parameter2.dat” that contains all the parameters including boron. I tried keeping this file in the main directory as well as in “packages” where original AD4 parameter files are there (in case the program reads from a particular directory).

Grid calculations do not have any problem. However, when I execute the autodock4, I get the following error.
autodock4: ERROR: unknown ligand atom type “autotypin”; add parameters first
autodock4: Edit the parameter library file AD4_parameter2.dat and try again
unsuccessful completion

I also tried changing the file name to “AD4_bound.dat” and with new parameters for all atoms and then included the command
Parameter_file AD4_bound.dat at the top of gpf and dpf files. Grid calculations are done with boron atom. Executing autodock4 will give the error.

I was just wondering why grid calculations take in the new parameter file, but docking does not recognize that.

Anybody has any solution/suggestions for this error?


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