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PostPosted: Tue Jul 03, 2018 1:04 pm 
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Joined: Tue Jul 03, 2018 12:46 pm
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There are a few questions that I would like to ask and have some discussion.

1) I would like to ask about the charge of aspartic acid in protein when using AutoDock. Is there any way to check the charge or pH setting? I use default parameter, so I have not set any pH when I prepare protein template or ligand. However, I have just realized that the hydrogen atom of carboxylic functional group of aspartic acid is missing at the beginning. There is no hydrogen atom in carboxylic functional group when adding hydrogen (before merging non-polar hydrogen). The atom type of both oxygens in carboxylic functional group are OD. Is it normal or should I fix this one?

2) Is it possible to see ionic interaction in AutoDock? For example, the interaction between carboxylate of aspartic acid and protonated amine.

3) I converted dlg file to pdb and open in MOE to see 2D interaction between ligand and amino acid. The non-protonated amine turned to be protonated form. I mean positive charge on nitrogen atom without hydrogen adding on it. Based on all of your experience, do you think this problem come from file converting, parameter setting, or some error from MOE?

Thank you
Nan


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