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<p style="margin-top:0;margin-bottom:0">Hello,</p>
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<p style="margin-top:0;margin-bottom:0">I noticed that the <span>lipophilic atomic potentials of OD2 and OE2 are set to very positive values in mlp.py: </span></p>
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<div> 'ASP': {'C': -0.54,</div>
<div> 'CA': 0.02,</div>
<div> 'CB': 0.45,</div>
<div> 'CG': 0.54,</div>
<div> 'N': -0.44,</div>
<div> 'O': -0.68,</div>
<div> 'OD1': -0.68,</div>
<div> 'OD2': 0.53}</div>
<div> 'GLU': {'C': -0.54,</div>
<div> 'CA': 0.02,</div>
<div> 'CB': 0.45,</div>
<div> 'CD': -0.54,</div>
<div> 'CG': 0.45,</div>
<div> 'N': -0.44,</div>
<div> 'O': -0.68,</div>
<div> 'OE1': -0.68,</div>
<div> 'OE2': 0.53},</div>
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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?
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<p style="margin-top:0;margin-bottom:0"><span>Zhijie</span></p>
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