FFTK Determination of Dihedrals to be Scanned

From: Zeki Zeybek (zeki.zeybek_at_bilgiedu.net)
Date: Sun Feb 26 2017 - 08:20:30 CST

I am using FFTK plugin in order to generate a parameter file for L(+) Lactate molecule. However in the last step of parameterization protocol even though I have several dihedral angles in the Scan Torsions tab it only shows one of them. I know this is pretty normal considering that FFTK ignores dihedrals ending with hydrogen. And my problem starts right there, I mean 1-) Why would one ignore dihedrals ending with Hydrogen 2-) How can I add the necessary dihedrals for my parameterization procedure and also how to decide which ones are necessary? 3-) I read the tutorial completely and even in the tutorial we had to add dihedrals manually, according which criteria ?. I appreciate any sort of help and also sorry for my ignorance on the matter.

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