On Sat, Feb 15, 2014 at 02:22:27AM -0800, anna wrote: > Dear all, > > I need to calculate electrostatic potential (ESP) derived atomic charges. I > did geometry optimization with MMFF94s force field. Is it also important to > do rotor search in order to minimize the molecule?
Usually an ensamble of random conformations is taken from MD trajectory and average charges calculated, e.g., using R.E.D. software [1]. Rotor search probably can get a good starting point. > > Another question that I have is if rotor search should be done before or > after geometry optimization. Probably the important thing is to choose the > lower energy structure independently if rotor search was did before or after > geometry optimization. > When you are calculating ESP the molecule should be optimized at QM level, so the initial MM optimizations (and rotor search) are only about getting at a good starting point. > Is rotor search also adequate for aromatic compounds like coumarin? > No. Rotor search is done only over rotable bonds (those that are not part of any ring systems or multiple bonds). Coumarin doesn't have a single rotable bond. Reinis [1] http://q4md-forcefieldtools.org/ ------------------------------------------------------------------------------ Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth, Mapview and more. Get your Android app in front of a whole new audience. Start now. http://pubads.g.doubleclick.net/gampad/clk?id=124407151&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
