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.
On Sun, Feb 10, 2013 at 10:10 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> 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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>
--
*With Best Regards
Subrata
PhD Student
Dept of Chemistry.
IIT G
*
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Received on Mon Feb 11 2013 - 03:00:02 PST
