I have modelled the structure using both ChemDraw and MarvinSketch separately. The structures were recognised as correct. However, once submitted into AutoDock, the torsion tree root cannot be detected and the Ir atom is marked as unknown, this is followed by failure to set the map types and eventually to run the simulation. I've tried using SwissDock, however once I submit the ligand, I am asked to review the topology. I have used the PRODRG server, however the Ir atom is not recognised by this software. Anyone has come across this sort of struggle?
In this case, you should follow the standard procedure for Autodock parameter file. Follow this links
1. http://autodock.scripps.edu/resources/parameters/AD4.1_bound.dat/view
2. http://autodock.scripps.edu/faqs-help/how-to/adding-new-atom-parameters-to-autodock
You may also follow this link
3. http://mgldev.scripps.edu/pipermail/autodock/2009-March/005439.html
Thanks.
Thank you for the links, I found the parameters I need. However, I cannot seem to locate the parameter file within autodock that I need to modify.
I've written new GPF and DPF files and reopened them via autodock, however once I try to run the docking I get a message 'ERROR: unknown ligand atom type Ir add parameters for it to the parameter library first!'.
I've noticed that the docking using Autodock-vina for metal based systems always returns this error as the parameters for metals in specific are incomplete in the GA algorithm used in Autodock. I would recommend using GOLD if you have a license or for an inexpensive means, pursue HEX docking. They are just as easy if not as quick as Autodock-vina.
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