Re: [AMBER] NMA(n-methylacetamide)

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Sun, 10 Feb 2013 17:40:31 +0100

Hi,

my feeling is that the charges of ACE & NME were defined in the
following paper:
http://onlinelibrary.wiley.com/doi/10.1002/jcc.540161106/abstract

However, the charges of these ACE & NME fragments were designed for
capping peptides/proteins and might not be suitable for NMA.

To get charges for NMA I would simply derive charges using... the NMA
molecule itself (conformation cis and/or trans); see in R.E.DD.B.
http://q4md-forcefieldtools.org/REDDB/projects/W-20/
http://q4md-forcefieldtools.org/REDDB/projects/W-21/
http://q4md-forcefieldtools.org/REDDB/projects/W-22/

regards, Francois


> I have saved my NMA molecule in amber ff12SB force field
> NMA=sequence{ACE NME}
>
> when I checked the charges for the NMA molecule in the reference JACS
> 1993, 115, 9620,
> It is different than the above.
>
> Why this is ?
> can any one suggest me?




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Received on Sun Feb 10 2013 - 09:00:02 PST