Molecular Docking Server

Transition metal
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Author:  qfb_ros [ Thu Oct 22, 2009 5:11 am ]
Post subject:  Transition metal

Hello! My ligand has a Cu atom and when I try to upload the ligand in pdb it displays:

Error: The following atoms are not allowed for docking calculations: Cu

so, no transition metals allowed?

thank you!

Author:  bikadi [ Thu Oct 22, 2009 9:32 am ]
Post subject:  Re: Transition metal


you are right - no transition metal atoms are allowed in the ligand. There are theoretical reasons behind this, because force fields are generally not capable to handle coordinative bonds. In case of octahedral Cu complexes the Cu is burried inside the molecule, so it will not inflence the docking results, you can simply omit it. However, it is not impossible to somewhat consider transition metals in ligands, we will consider to develop this function in DockingServer in the future.


Author:  jhanks1981 [ Wed Feb 15, 2012 9:42 pm ]
Post subject:  Re: Transition metal

No Selenium allowed either?

Author:  bikadi [ Thu Feb 16, 2012 11:53 am ]
Post subject:  Re: Transition metal

No, unfortunatelly Selenium is not allowed, there is not enough experimental data to create reliable parameters for selenium, I suggest to use sulphur instead.

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