I want to understand force field ( if possible to make again one of them), For beginning i read past article about force field , for example worked by "Cornell" (A second generation ff... 1995) or "Weiner ,Kollman" (An all atom ff...1986) and ...
Most of them have the same equation but a little different in parameter, when I want to calculate energy for a molecule I don't know the value for "r" , Angel (for example).
because if I put in the eq value, the three first terms be zero so its irrational.
So if anyone has knowledge about this area I'm grateful if you share.
Akbari
Each term describes the energy relative to the chosen reference state. The reference state for each interaction is at its defined equilibrium angles, distances, which can be parametrised e.g. using quantum chemical calculations.Of course, for a more complex system than a diatomic gas, since the total energy is summed up for all different interactions of the system, with a lot of different reference states that are generally incompatible with each other, it cannot possibly be equal to zero for any configuration. Furthermore, it refers to a comparison with a state of free, non-interacting molecules with non-interacting fragments at 0 K.
A recommended text book for beginners: Jensen, Frank; Introduction to computational chemistry, Wiley, 1999.
I would not recommend that you do this: it will takes years of work, and you will only be re-inventing a wheel that already works pretty well.
Check out:
http://www.ks.uiuc.edu/Research/vmd/
http://www.gromacs.org/
http://ambermd.org/
http://www.yasara.org/
Hi prof Bywater
I'm agree with you,but my prof want to know its possible to do it and use it in docking, actually my field study is Chemometrics and i worked in molecular docking with Glide (Schrodinger),Gold (CCDC), FlexX and Autodock, we write Searching algorithm and we need force field for scoring function.
So you say its time consuming and irrational, but its possible use current FF package in our program?
Best regard.
Akbari
You already seem to have all the equipment that you need: Glide (Schrodinger),Gold (CCDC), FlexX and Autodock. They will do the docking for you. If you later want to improve the docking, calculate energies etc. you can do that using GROMACS, AMBER; VMD, CHARMM etc. These programs will also allow you to do QM/MM calculations. I don't think it would be a profitable use of your time to write new programs that do these things, the software is probably as good as it will ever be.
Your point of view absolutely its true, but we want to use this (Conformation )energy calculation in Matlab (we write good (searching)algorithm and we can change it )so in my perspective we can't use these packages in Matlab. Since we should write it. if you have suggestion about it I'm grateful.
Best regards.
Akbari
OK. You didn't make that clear - you want to implement all this in Matlab.
It can almost certainly be done, but it is still a huge task The algorithms are all published and you can get a lot of the source codes (usually in C or fortran) which you would then have to convert into Matlab "language".
I would still not recommend that you do that, it will use up too much of your life!! But what you can do in Matlab is write a script that invokes various routines from the programs that I mentioned, control the perfomance of the calculations and then delivers results in Matlab formats.
Good luck !
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