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2262	Improve MLP lipophilicity parameters	zhijie.li@…	Tom Goddard	"From: Zhijie Li 
Thu Jul 11 21:48:09 PDT 2019
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Hello,


I noticed that the lipophilic atomic potentials of OD2 and OE2 are set to very positive values in mlp.py:


 'ASP': {'C': -0.54,
         'CA': 0.02,
         'CB': 0.45,
         'CG': 0.54,
         'N': -0.44,
         'O': -0.68,
         'OD1': -0.68,
         'OD2': 0.53}
 'GLU': {'C': -0.54,
         'CA': 0.02,
         'CB': 0.45,
         'CD': -0.54,
         'CG': 0.45,
         'N': -0.44,
         'O': -0.68,
         'OE1': -0.68,
         'OE2': 0.53},


As as result the hydrophobic surface representation always show hydrophobic patchs on the carboxylates, which look quite odd to me.   Is there a justification for this setting?  In addition, aren't the two oxygens in the carboxylate equal considerting that they are in resonance?


Zhijie"	enhancement	closed	moderate		Structure Analysis		fixed		Elaine Meng				all	ChimeraX