Entering edit mode
7.9 years ago
Hassan Rasouli
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10
How can I add an ions to a peptide in pdb file? I will add a copper or zinc ions to a peptide with 27 aa length. which software is better than other for this aim?
It is unclear what you are asking, are you trying to edit a PDB file? The main question is not the technical one though, but to determine a suitable site. I'd read a few reviews on the topic first, e.g. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2144590/
Dear Dr.Michael Dondrup Thank you very much. That's very kind of you. Really I will add a ions to a pdb file. This pdb file is related to a peptide. I think that I will need to your more help. Would you can send me your email for receiving more guidelines from you about this issue? Yours sincerely, Hassan Rasouli Kermanshah University of medical science, Iran. H3n.rasouli@gmail.com
Let's keep this on Biostars. Also, I'm likely not the right person to help you, I just asked for clarification. Just adding the ions to a PDB file doesn't make much sense though, if you don't know if the ion binds at all or where there are potential binding sites. I don't have more protocols for this purpose except for trying molecular docking simulations and tools like WebFeature http://feature.stanford.edu/.
See e.g. https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html for an intro to the PDB format.
Thanks! I find my answer! By changing original pdb file and put ions coordinate in the correct position in the pdb file we are able to do it. for this propose I used the http://blue11.bch.msu.edu/mmtsb/Mutate.pl. I think this is better than Modeller for create any change in original pdb file I hope best wishes for you Yours sincerely, Hassan