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
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Mon Mar 15 2010 - 09:00:02 PDT
