[AMBER] Partial charge discrepancy between AM1-BCC small molecule charge and FF library charges

From: Liao via AMBER <amber.ambermd.org>
Date: Thu, 28 Jul 2022 04:45:03 +0800

Dear experts,

Today when looking at partial charges on my molecules, I found quite a big difference, between the side chain N on Lysine, and an alkyl NH3+ on a small molecule. The small molecule has its partial charges calculated by sqm in UCSF chimera for AM1-BCC charges, and the Lysine charges are from ff14SB library.

I drew the standalone lysine and added charges to it, and the big difference still stands, that the side chain N on Lysine is +0.374 (in NH3+ state), and the newly calculated lysine treated as a small molecule is +0.851. Changing the small molecule lysine from NH3+ to NH2 the non-protonated state didn't make a significant difference, that the recalculated charge after minimization is +0.909.

I remember from reading, and from my own experience, that good charges are one of foremost important factors in modeling. So I'm quite surprised by this difference, that AM1-BCC charges are known to be good, and so are well established FF charges, but they differ so much in the case of NH3+.

Which one should I prefer?

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Received on Thu Aug 04 2022 - 13:37:29 PDT
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