I also think it's very important. There are several reasons:
- I could use an off-the-shelf forcefield for building molecules. Nothing special, just to relieve the worst strain in an initial configuration
Right - it will certainly be an enrichment of CDK's functionality. I'm also thinking about making it flexible enough to work with 2D and 3D equations and parameter sets in order to supplement SDG.
- We are currently discussing the abstraction of forcefields at fsatom.org. I suspect this is too large a topic, but I am interested in the idea of reading in a functional form and generating code to support that. Not everyone agrees
I was not aware of this site and project. Sounds interesting. Subscribed.
The idea that you sketch sounds great but would certainly be at least one full Ph.D. thesis, I suppose.
Can we assume that if the atomTypes are known then the construction of the FF is algorithmic? i.e. something like:
- assign atomTypes
- iterate through structure identifying:
bonds
angles
dihedrals
oop
non-bonded contacts
electrostatics
- assign numeric parameters to each of the above based on:
- a lookup table of allowed atomType combinations
- or values calculated by interpolation
This should all be automatic.
Exactly like this.
The you need to decide: - do you want derivatives? - do you want second derivs?
I'm not an expert here but from some basic reading I'm getting the impression that, for the really fast and simple minimization routines like steepest decent one needs first order derivatives. Simulated Annealing does not need them, but is certainly slower and more difficult to parameterize.
I think if this is a CS student they should concentrate on the numeric stuff and not so much time on crafting the forcefield to fit reality.
We do not intend to do the latter. We need something basic which works and which potentially is a starting point for later optimizations. I guess the 20 weeks might just be enough to get a very basic but functional version of our engine.
So this would be very useful and hopefully could be called with a single method (customisable if necessary).
Absolutely. Something like
interface ForceFieldEngine
{
public setMolecule(Molecule m);
public Molecule getMolecule();
public minimize();
// or maybe just?
public Molecule minimize(Molecule m)
public setParameters (ForceFieldParameters ffp);
}class DreidingForceFieldEngine implements ForceFieldEngine
{
}Cheers,
Chris
-- Dr. Christoph Steinbeck (e-mail: [EMAIL PROTECTED]) Groupleader Junior Research Group for Applied Bioinformatics Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de) Z�lpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786
What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3..
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