Problem With Enegry Miniization
Energy minimization prior to docking any small molecules is must. Most of the database does not contain the ideal coordinates of the small molecules thus it is must to correct them. Which method should we use to minimize their energy so that we can use them for any docking program? Please guide me. Thanks
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Dollas Salleh •
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Please try to improve this question. There are 2 spelling errors in the title alone. The question is vague, general and difficult to answer in its current form. Question will be closed unless you make some effort.
This also seems like an awfully formulated homework question...
Regardless, the question actually makes some sense in the current way, but it's more of a long answer than a straight to the point.. there are plenty of methods (steepest descent, conjugate gradient, newton-raphson, ...) used for energy minimization and they have different applications.
To get a better answer, include the following in your question: which molecule do you want to minimize? Small molecules or the receptors? Which level are we looking at (QM or MM)? Etc..