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-- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Candidate 352-392-4032 On May 28, 2012, at 9:53 PM, Bill Miller III <brmilleriii.gmail.com> wrote: > With the single trajectory protocol, all of the internal energy terms > cancel out because the coordinates for the complex, receptor, and ligand > are exactly the same. So if you sum those terms for the receptor and > ligand, the sum will always be the same as the corresponding terms for the > complex (as long as you have consistent parameters across all prmtop > files). However, the internal terms are calculated and do contribute to > delta G binding if the triple trajectory approach is applied, where a > different trajectory is supplied for the complex, receptor, and ligand. > > I hope that helps. > > -Bill > > On Mon, May 28, 2012 at 2:02 AM, Xioling Chuang <xioling_c.hotmail.com>wrote: > >> >> Dear All, >> >> For calculating the G total using mmpbsa.py of AmberTools 1.5, the G total >> is the sumation of G gas and G sol. However, it seems that only VDWAALS and >> EEL terms are tanken into account for G gas, not internal energy terms >> (bond, angle, dihedral, 1-4VDW and 1-4EEL). Is this reasonable for G gas >> calculation? If so, how can the internal terms contribute to G binding? >> >> Best Regards, >> Xioling >> >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> > > > > -- > Bill Miller III > Quantum Theory Project, > University of Florida > Ph.D. Graduate Student > 352-392-6715 > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Mon May 28 2012 - 16:00:02 PDT