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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>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
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Received on Thu Nov 01 2012 - 07:30:05 PDT
