sol66 said:
I actually have gromacs ... but gromacs requires me to parameterize the bond lengths for my chromophore.
Normally, you can determine these things from IR/microwave spectra of simple molecules. But chromophores can be quite large. I'm doubtful. How would you find and identify the modes of the respective bonds among all those peaks?
My group seems to be using MM for simulating the energy level of the chromophore which seems a bit silly to me since it doesn't take into account quantum mechanics of an sort.
That depends entirely on the context. MM methods are only as good as their parametrization, but when they're used for what they're meant to be used for, they're generally more accurate than most QM methods.
But obviously you can't use an MM method to parametrize itself, and an MM method is not more accurate than the QM method used to calculate the parameters.
But I wouldn't put the study of light-absorption in prosthetic groups to the category of things well-described by MM
at all.
What exactly are you (ultimately) trying to calculate? The actual light absorption process?
The difference in conformational energy? (assuming there's a conformational change) etc.
Currently I'm using this free program called ABINITI which is very nice. It'll do all the calculations for me for quantum mechanic bond lengths and such. Though I'm thinking to switch from my gromacs forcefield to something else that can do more accurate calculations. I've never done quantum chemistry,... so this is all very new and self taught.
As a quantum chemist, I can tell..
But I'm obliged to say that QC methods aren't 'black box methods'. Anyone can download a program, read the manual, and use it. But you can't get meaningful results without knowing what you're doing. The software is relatively easy to use, but they don't come with any safety-nets whatsoever.
There are plenty of good textbooks to learn the basics and underlying theory from. But if you haven't worked with it before, I'd suggest you might want to find an experienced quantum chemist to collaborate with before using it in research. There's just a heck of a lot of stuff the books won't teach you. Which method (at the moment!) is the most accurate, but still computationally-feasible, for your problem? What's the error for energy? For geometries? What's a good model size, and what should the model look like? In general: How should you go about doing the calculations, practically? What corrections, interpolations and other additional things might you need to do? Is the result even correct? How do you tell if it converged to the wrong wave function or geometry? Etc. These days, there's a lot of papers being published where, frankly, people simply didn't know what they were doing.
Now, I don't mean to dissuade you! I'm happy to see more people do quantum chemistry. It's just doing quantum chemistry without knowing quantum chemistry that I'm wary of. Bad results are just a waste of time for everyone involved, after all. As I said, QM methods aren't always more accurate than MM methods. (or rather, they're generally
less accurate, since MM methods just aren't used, or shouldn't be used, where they're not well-parametrized) As chemisttree notes, you also have QM/MM methods (I've used some myself). If you want to, say, try to reproduce light absorption in the chromophore, followed by some conformational change in chromophore and a larger-scale conformational change in the protein, that would be your only choice (if you could make it work).
If you wanted to calculate the change in energy of the entire protein after a change in the chromophore (skipping the actual absorption process), you could do that with MM alone,
but it's very difficult to get an accurate value there. A protein has thousands of degrees of freedom, and correspondingly many local minima on its potential-energy surface. How do you know your energy is being being calculated relative the correct states? (E.g. say an unrelated part of the protein was 'stuck' in a local minimum that's high in energy, and and moved down to a lower one during your optimization, thus giving an apparent drop in energy that's larger than it should be) if you only want to study a conformational change in the chromophore itself, on the other hand, you may well be better off with a pure QM calculation, because there's no problem finding the correct energetic-minimum conformations for a smaller system.
I'm happy to give a suggestion, but it all depends on what you're actually trying to do in the end.
