Dear Bill and Jason,
Thank you very much for your explanations. It's clear for me now.
Best Regards,
Xioling
> From: jason.swails.gmail.com
> Date: Tue, 29 May 2012 08:31:43 +1000
> To: amber.ambermd.org
> Subject: Re: [AMBER] why is internal energy not taken into account for G gas?
>
> As a supplement to Bill's response, you can set verbose=1 (maybe 2, check the manual to be sure) to have MMPBSA.py include the internal terms in Ggas.
>
> They are only omitted, however, if they do appropriately cancel for delta G of binding. I think this is described in the Reference manual for AmberTools 12.
>
> HTH,
> Jason
>
> --
> 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
> >>
> >>
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> >>
> >
> >
> >
> > --
> > 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
>
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Received on Tue May 29 2012 - 19:30:02 PDT
