AMBER Archive (2009)

Subject: Re: [AMBER] LYN again

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Mon Apr 06 2009 - 09:26:14 CDT

Marius,

> The above representation got messed up, so I'm going to explain it. The
> linker has on both ends the C=O group, so what I called linker are just a
> few carbon and nitrogen atoms. Between this C=O and the NZ-H of the lysine I
> have a peptidic bond.

Yes, sorry... I realized once I sent the email that your linker was
CO-R-CO (and not NH-CO-NH).

Anyway, your target molecule is still:
  ACE-NHCH(R)CO-NME with R = (CH2)4NH-ACE (ACE = MeCO; NME = MeNH)

> Apparently, even for LYS residue, only two conformations where used for
> deriving the charges in the original paper.

Yes

regards, Francois

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