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From: Jason Swails <jason.swails.gmail.com>

Date: Thu, 2 Dec 2010 12:27:32 -0500

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
*

*>
*

Date: Thu, 2 Dec 2010 12:27:32 -0500

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:

-- 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/amberReceived on Thu Dec 02 2010 - 09:30:04 PST

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