Dear All,
I have newly started working with molecular docking using AutoDock software package. In my work, I am trying to study interaction between Dy2O3 and HSA. While running the complex structure (Dy2O3-HSA) I am having trouble with the Dy element. In my work, I am trying to study interaction between Dy2O3 and HSA. While running the complex structure (Dy2O3-HSA) I am having trouble with the Dy element.
When I try to run autogrid, I am getting the following error message "Parse error on line 7 in file "DY2O3.pdbqt": ATOM syntax incorrect: "DY" is not a valid AutoDock Type. Note that AutoDock atom types are case sensetive."
If anyone suggests to me how to resolve the issue, it will be very helpful. I am trying to study binding of a couple of compunds containing Dysprosium and Holmium.
Thanks in advance.
Regards
Sumantra
Hello Sumantra,
The issue is due to AutoDock’s limitation in handling non-standard elements like Dysprosium (Dy) and Holmium (Ho). AutoDock is primarily designed for organic molecules and proteins, and it does not natively support rare-earth elements or their oxides (e.g., Dy₂O₃).
AutoDock requires atom types to be defined in the AD4_parameters.dat file. Since Dy and Ho are not included by default, you’ll need to add them manually:
Add new entries for Dy and Ho under the atom_par section. You can use parameters similar to other heavy metals (e.g., Zn or Fe) as a starting point (You most likely need to refine these parameters based on experimental or theoretical (QM-derived) data for Dy and Ho.). For example:
atom_par Dy 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
atom_par Ho 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
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