you need to look at the Amber web site that I pointed out before. Don't rely
on wikipedia, use the official Amber site.
On Mon, Mar 15, 2010 at 10:32 AM, Whimsica.aol.com <whimsica.aol.com> wrote:
> The equation on wikipedia has electostatics torsions angles bonds...
> Parm99 has only 2-3 parametrs and they are not labeled. Same with the
> allnuc94 how do I tell which number corresponds to which parameter in the
> wikipedia equation
>
> Thanks for any guidance
>
> Dan
>
>
> On Mar 15, 2010, at 7:47 AM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> they are available for download on the amber web site (www.ambermd.org),
>> along with a lot of information on the format. make sure to compare
>> energies
>> and forces from your code to that from Amber- there are multiple examples
>> in
>> the past of people using "Amber" force fields, but not doing the
>> conversion
>> or calculation correctly.
>>
>> On Mon, Mar 15, 2010 at 8:46 AM, <whimsica.aol.com> wrote:
>>
>>
>>> I'm writing a small molecular dynamics system for students and would like
>>> to try using amber forces in a simulation.
>>> On wikipedia it says that the amber force field can be calculated using
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> and the parameters of the force field (e.g. force constants, equilibrium
>>> bondlengths and angles, charges). Peptide, protein and nucleic acid
>>> parameters are provided byparameter sets with names beginning with "ff"
>>> and
>>> containing a twodigit year number, for instance "ff99"
>>>
>>> Could someone please point me to the parameter file(s) that would
>>> including
>>> everything necessary to use this equation.
>>> I'm writing a small molecular dynamics system for students and would like
>>> to try using amber forces in a simulation.
>>>
>>> Thanks,
>>>
>>> Daniel Savage
>>> CinematicSciences
>>>
>>>
>>> _______________________________________________
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>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Mon Mar 15 2010 - 09:00:03 PDT
