Hello everyone..
I am new in autodock4 and when i am preparing the ligand as pdbqt ( add polaronly, computing Gasteiger charges and merge non-polar), i am getting warning msg that say (these atoms have zero charge: Re Cl) .
so when i open this PDBQT file by ADT, i see that some bonds have not visualised, as Re-Cl , Re-N
am unable to understand how to plot these bonds ??
please help me
Hi Yassine,
AutoDock does not have force field parameters for Re,
so Re-Cl and Re-N bonds are not visualized in ADT.
http://autodock.scripps.edu/faqs-help/faq/where-do-i-set-the-autodock-4-force-field-parameters
Sir Yoshinobu,
my ligand of general formula " fac-[Re(CO)3 Cl (k2-L)] "
So i have already added the atomic parameters of Re in parameter library of ADT in the first moment, and i have tried replace the 'Re' by 'Mn' in same construction , but i get the same warning.!!
It's possible that I have made a mistake in something, or that I did not know how/where to add this parameter in modified parameter file !!.
It would be kinder if you show me the steps to add this atomic parameters file.
thanks
Hi Yassine,
AutoDock is able to handle metalloproteins containing Fe, Mn, or Zn as a receptor,
but is not able to do metal complexes as a ligand, so you got the warning.
Hi Yoshinobu..
I have an exampl. In the following paper, he worked with Re-complexe, so i think that AutoDock is able to handle these ligands. (These ligands looks like that I have)
Hi again,
You can check the following archives:
https://www.researchgate.net/post/How_can_i_do_docking_Selenium_or_any_other_metal_as_Ligand
https://www.researchgate.net/post/Error_in_docking_copper_containing_proteins_by_Auodock4
http://mgldev.scripps.edu/pipermail/autodock/2009-March/005439.html
Good luck!
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