Dear Jason,
If it is the case, how can I calculate the interaction energy between residues wiht AMBER?
Best regards and many thanks,
Cat
> Date: Thu, 2 Dec 2010 12:27:32 -0500
> From: jason.swails.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] Please help! MM-GBSA per-residue energy calculation.
>
> Sorry, I meant to reply to this one. I'll just post my response from the
> other email.
>
> Per-residue decomposition does not measure interactions *between* residues
> (that is the pair-wise decomposition scheme). Each residue has an intrinsic
> energy due simply to the other atoms within that residue. For instance, the
> bond, angle, and dihedral potential terms that arise from from atoms within
> that residue belong to that residue's self-energy, as do the 1-4 EEL/VDW
> terms and the other non-bonded energy terms from atoms connected by more
> than 3 bonds. There's nothing wrong with getting a self-energy (in fact,
> you should) for per-residue decomposition.
>
> Now we come to the DELTA part. This is simply the energy of that residue in
> the complex less the energy of that residue alone. Therefore, the bonded
> potential terms (i.e. the bond, angle, dihedral, and 1-4 interactions)
> should be the same in both if you used a single trajectory to get all of
> your snapshots, so those should cancel exactly. However, the exposed
> surface area should be considerably greater, since it's no longer buried, so
> that potential term should add considerably to the DELTA. Also, the
> isolated ligand does not have any electrostatic interactions with other
> protein residues, like it does when it's in the complex, so you will see a
> difference arise there as well.
>
> Hope this helps,
> Jason
>
>
> On Thu, Dec 2, 2010 at 11:43 AM, Catein Catherine <askamber23.hotmail.com>wrote:
>
> >
> > > Dear All,
> > >
> > > I have done MM-GBSA calculation for a protein-drug complexes.
> > >
> > > I found the total DGtot = -60.
> > >
> > > Then, I use the per-residue option in MM-GBSA. I found the following data
> > in the Delta section.
> > >
> > > residue....SINT....BINT...TINT....TGBTOT
> > > 1
> > > ..
> > > ..
> > > ..
> > > ..
> > > 500 ......................................................
> > > drug.............................................-32
> > >
> > > However, when I sum up all the TGBTOT from residue1 to residue500. I
> > found the energy sum is about -30. In addition, I found the drug has TGBTOT
> > value of -32 too.
> > >
> > > I am not sure if I understand correctly, is the total binding energy of a
> > drug (read from the per-residue result page) equals to -30 (from residue 1
> > to 500) plus -32 (from the drug).
> > >
> > > However, I cannot quite understand why the drug could have -30
> > interaction energy with itself. How can I interprete the data?
> > >
> > > Please kindly help.......
> > >
> > > Best regards,
> > >
> > > Catherine
> > >
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> >
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> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
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Received on Fri Dec 03 2010 - 00:30:03 PST
