[MMTK] Adding/modifying forcefields

david.evans at ulsop.ac.uk david.evans at ulsop.ac.uk
Fri Dec 17 16:49:02 CET 2004


Hi Guido,

Thanks for the reply. I was hoping that I could use the existing
Amber94 classes, and just change the input parameter files, i.e. use
something instead of 'amber_parm94'. The functional form of Amber99
and gaff is identical to Amber94, I believe, so I thought it  would
just be a question of ensuring the correct data was read in.

Sorry if I'm being dumb, but I've only spent a couple of days playing
with MMTK and don't really understand the code base at all.

thanks

Dave

---- Message from Guido Wagner <wagner at chemie.uni-frankfurt.de> at
2004-12-17 15:49:18 ------
>Hi Dave !
>
>You will have to write your own class for the forcefiled. There is
no need to 
>modify existing code. The example for the harmonic Oscillator ff,
that comes 
>with MMTK is a good way to get started. After that you should have a
closer 
>look at the Amber94 implementation. It uses the following approach:
>
>The universe class is derived from a forcefield class which
implemets a method 
>called evaluatorTerms, which iterates over the objets in the
universe and 
>builds a list of energyterms to evaluate. An other method
(energyEvaluator) 
>evaluates the list of energyterms (this functionality is split up in
split up 
>in subclasses, but I will not discribe this here). An element in the
list of 
>energyterms consists of a "reference" to the evaluation code (here 
>implemented in c) and the necessary data.
>In the c part you will find the actual ff code (calculation of
energy and 
>derivates [ for the energy minimizer ] and lots of "book keeping"
code, that 
>is important to understand, if you want to be compatible to other
MMTK 
>modules like the energy minimizer. I think you should try to extend
the 
>Amber94 ff for your needs. Good Speed !
>
>Guido Wagner
> 
>
>Am Freitag, 17. Dezember 2004 13:20 schrieb david.evans at ulsop.ac.uk:
>> Hi,
>>
>> I'd like to use the Amber99 ff, in conjunction with gaff to
describe
>> ligand binding energetics.
>>
>> I have, I think, understood how to create new molecules using
>> database files in
>> .mmtk/Database/Molecules
>> and would like to do something similar for forcefields i.e. without
>> modifying the base distribution.
>>
>> Thanks
>>
>> Dave
>>
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