*Hi *Gustavo,
*Thank you for your suggestion, i will try it (an read the GAFF paper too)*
*
*
*SA*
2012/11/1 Gustavo Seabra <gustavo.seabra.gmail.com>
> Your best option would be to look here:
> http://dx.doi.org/10.1002/jcc.20035
>
> But, assuming that by TMAO you mean Trimethylamine N-oxide:
> http://en.wikipedia.org/wiki/Trimethylamine_N-oxide
>
> My *guesses* would be:
> * sp3 nitrogen with 4 substituents: ==> n4
> * What looks like and oxygen in a hydroxyl group ==> oh
>
> HTH,
> Gustavo Seabra
> Professor Adjunto
> Departamento de Química Fundamental
> Universidade Federal de Pernambuco
> Recife - PE - Brasil
> +55-81-2126-7450 x5023
>
>
>
> On Nov 1, 2012, at 11:05 AM, sa wrote:
>
> >>> I believe you mean ff99SB, right?
> > Yes indeed I mean ff99SB,
> >
> >>> Have you tried to use GAFF?
> > For the first test i would prefer to use ff99SB, since this force field
> and
> > GAFF have a lot of common parameters. So in ff99SB or GAFF, what are the
> > best for N and O atoms for TMAO?
> >
> > Thank you again for your response.
> >
> >
> > 2012/11/1 Gustavo Seabra <gustavo.seabra.gmail.com>
> >
> >> Have you tried to use GAFF? And, I believe you mean ff99SB, right?
> >>
> >> Gustavo Seabra
> >> Professor Adjunto
> >> Departamento de Química Fundamental
> >> Universidade Federal de Pernambuco
> >> Recife - PE - Brasil
> >> +55-81-2126-7450 x5023
> >>
> >>
> >>
> >> On Nov 1, 2012, at 9:39 AM, sa wrote:
> >>
> >>> Dear all,
> >>>
> >>> I would like to use (in the first approximation) the Amber ff99 force
> >> field
> >>> to simulate TMAO in water In your opinion, what are the best atom types
> >>> available in this force field for the N and O atoms
> >>>
> >>> Thank you for your help
> >>>
> >>> SA
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Received on Thu Nov 01 2012 - 08:00:04 PDT
