Checking something on a friday evening wasn't such a good idea :).
So te be very clear:
this parameter is still in de amber9.ffparms on
(
http://amber.scripps.edu/dbase.html):
X -n3-p5-X 6 18.000 180.000 2.000
but also:
c3-n3-p5-o 1 3.00 180.0 -2.
c3-n3-p5-o 1 2.30 0.0 3.
Second of this seems ok (depending with forceconstant you give to the
other 5 dihedral angles), togheter they make a bit more complex curve.
Other comment on the angles still stands.
Sorry for the confusion, so 3 problems in the gaff:
X -n3-p5-X 6 18.000 180.000 2.000
o -p5-o 46.0 115.80 SOURCE3 17 4.6921 5.7902
o -p5-oh 43.8 115.03 SOURCE3 86 3.5330 4.9414
Mistake or do I look at them in the wrong way?
servaas
Quoting Servaas Michielssens <servaas.michielssens.student.kuleuven.be>:
> I just noticed that I did not download the latest gaff.dat file. There
> are other more realistic parameters in there.
>
> Sorry for my to fast post.
>
> greetz,
>
> servaas
>
>
> Quoting servaas michielssens <servaas.michielssens.student.kuleuven.be>:
>
>> Dear,
>>
>> I was making a new topology for a molecule that contains a P-N
>> bound, I used the gaff.dat file to generate the new paramters. When
>> I had a look at the new paramters the gaff parameters for the
>> X-p5-n3-X in the gaff suprized me:
>> X -n3-p5-X 6 18.000 180.000 2.000
>>
>> I expected:
>> 1. the forceconstant value to be much lower
>> 2. the phase to be 0
>> 3. pn to be 3
>>
>> So I decided to recalculated the parameter for the molecule in the
>> attachement, I followed the strategie as in J.comput chem 24:
>> 1016-1025, 2003.
>> Results point out that the function is nothing like the parameters
>> in the gaff but a much more complicated function. It cannot be
>> fit with 1 cosine function (which is no problem of course) and
>> barriere is +/- 2kcal/mol (Vmax).
>>
>> Their was also another problem:
>> gaff:
>> o -p5-o 46.0 115.80 SOURCE3 17 4.6921 5.7902
>> parm99.dat:
>> O2-P -O2 140.0 119.90
>> Their must be something wrong with the force constant in the amber
>> gaff.dat here (or my interpretation of them)...
>> same for:
>> o -p5-oh 43.8 115.03 SOURCE3 86 3.5330 4.9414
>>
>>
>> Sincerely,
>>
>> servaas michielssens
>
>
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Received on Sun Feb 24 2008 - 06:07:51 PST
