Hello everyone,
I need your help please
I am docking a mixed complex with a coordinence of 6 using autodock vina.
Once the calculation is done, I can't visualize the interactions because my complex is decomposed. I even used other programs like ligplot and protein plus server. They gave me the interractions of one of the ligands with the protein but not the whole complex. Knowing that the complex was optimized by DFT and saved in .pdb to be used for docking.
Thank you.
Hasnia Abdeldjebar Assalam o alaikum wa rahmatullahi wa barkatuhu
Hope you doing well
Share your complex.
Hai Hasina,
Try in discovery studio or else, if u provide the output file we can look over it.
In general, docking programs can't handle complexes with transition metals (or even metals in general), as there are no parameters for such elements. If, however, docking works fine (there are ways to add parameters of specific elements to e.g. autodock) then it's most likey just a problem with visuzalization, as probably ligplot can't handle drawing metal complexes (likely won't draw any bonds within the complex). The results may be still OK, but it just a matter of proper visualization. Try visualizing the output poses e.g. in PyMol or Maestro, where you can add missing bonds.
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