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Docking ligands in an active site with metal ions
http://mgl.scripps.edu/forum/viewtopic.php?f=9&t=3388
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Author:  occehc [ Thu Feb 09, 2017 12:29 am ]
Post subject:  Docking ligands in an active site with metal ions

Hi,
I am trying to dock some ligands in an catalytic site containing a Mg ion using Autodock4. All the ligands are though to interact with the metal ion as they contain a metal-binding motif. I am aware that I can specify the Mg charge manually in the pdbqt file, and I know that a charge of +2 is probably not accurate as the partial charge would change due to the surrounding residues. I found this paper which is very useful

https://www.ncbi.nlm.nih.gov/pubmed/17311351

As it deals with a similar problem by trying with different charges on the ion. What I would like to discuss with someone that has more experience in this is how to decide the correct charge on the Mg ion, I see that in the paper they discarded the +2 charge due to the short distances between the ion and the oxygens, but I am not sure how to decide a cutoff for this and/or if there are other strategies that people are aware of. Thanks in advance,

Francesco

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