AMBER Archive (2006)

Subject: AMBER: Nature of QM scanning protocol for parameter development

From: Isherwood, James (james.isherwood_at_imperial.ac.uk)
Date: Fri Aug 11 2006 - 11:17:01 CDT

Dear list,

I have been attempting to develop missing paramaters in the ff99 for a selenomethionine (MSE) residue. My question concerns the nature of the QM scanning protocol. Using g03, I am under the impression that one should use a relaxed scan for probing the energy profile of the selenium bonds and then fit a harmonic term to this. I want to know why one should use a relaxed scan versus a rigid one, since I would think that there would not be sufficient time for the molecule to relax during vibration. I have been looking but have yet to be convinced with an answer, is anyone able to shed more light on it?

James

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