Re: [AMBER] NMA(n-methylacetamide)

From: Jason Swails <>
Date: Mon, 11 Feb 2013 06:01:19 -0500

On Mon, Feb 11, 2013 at 5:31 AM, Subrata Paul <>wrote:

> Dear
> D. A. Case,
> The charges for ACE and NME are given in the JACS 117:5179, 1995.
> so, Is making NMA molecule by sequencing ACE and NME create any problem ?
> and again, from Dr. FyD, reply
> he said that , sequencing ACE and NME is not suitable for NMA.

> please suggest.

Francois provided a suggestion. If you are that worried about the charge
definition of NMA, then you might as well rederive charges for the whole
molecule. The existing residues had charges derived as capping residues
(as Francois pointed out). What this means is that the charges of ACE and
NME were constrained to give the appropriate charges to the amino acid
residues. Since these constraints would not be present in the charge
derivation of a pure NMA molecule, you could probably get a better RESP fit
by refitting charges.

Good luck,

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Mon Feb 11 2013 - 03:30:02 PST
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