I want to perform docking onto a calcium-dependent protein. Based on x-ray crystal structures, these calcium ions do not bind directly to ligands, but they do help in maintaining the structure of the protein so that the protein can function well.
My questions are:
1) Should I include these calcium ions in docking process?
2) If yes, how would I achieve that? I have tried to generate the PDBQT file, but it put the calcium ions to be zero charges.
You can just have a try, with or whitout the calcium ions!
The charge of Zn in PDBQT file, I think, can be modified by hand. See the paper www.ncbi.nlm.nih.gov/pubmed/17311351.
In the PDBQT file, change zero charges of the calcium ions to be 2. It may be helpful.
Adding to the above, please see this thread:
https://www.researchgate.net/post/How_can_we_change_the_partial_charge_of_a_pdbqt_file_in_autodock
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