I work in molecular docking,actually i try to make docking program in Matlab, my searching algorithm write in Matlab but i have problem to find force field for interaction calculation(scoring).
So if you know a way to use current force field with or in matlab or make link between there?
I didn't get exactly your question. Are you looking for Matlab code? If so, did you try MatlabCentral?
If it is about potential fields try finding out about quiver function...
even electrostatic and magnetic field related functions will be included in the same library
Molecular docking program contain two important part:
the first one its " Searching Algorithm" that try to find best posing (or orientation) of ligand conformation in active site of targets and the second one its "Scoring function" that score the posing of ligand in active site.
We write Searching algorithm for our work but now we have problem with scoring function, one of the methods in Scoring its Force Field (like Amber, GROMOS , CHARMM , MM3 ) that use molecular mechanics calculation to calculate interaction between ligand and protein. most of this FF write in C++ or others like FFX that write in Java. the last one is open source and i want to use it in Matlab with my searching algorithm.
I'm working on this issue. I am using the software Autodock 4.2 & Autodock vina. I couldnt find the best conformation of ligand . In fact I use genetic algorithm and I couldnt create my chromosom.(Can You advice me what should I do to find best conformation?)
(for scorinf function) : I guess by calling cmd in matlab environment and run some rules you can calculate the energy. The following link can help you get your answer.
https://www.biostars.org/p/106938/
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