You can calculate the pairwise interaction energy between residues by
setting idecomp=3 or 4 with MMPBSA.py or DCTYPE = 3 or 4 with mm_pbsa.pl.
Either of these two settings will calculate the pairwise interaction
energies. See the Amber manual for more details about the differences
between these two values.
Good luck!
-Bill
On Fri, Dec 3, 2010 at 3:01 AM, Catein Catherine <askamber23.hotmail.com>wrote:
>
> 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
> > > >
> > > > _______________________________________________
> > > > 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/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > 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/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Fri Dec 03 2010 - 04:00:03 PST
