Re: [AMBER] editing parm in LEAP

From: Jason Swails <>
Date: Thu, 2 Dec 2010 12:26:44 -0500

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,

On Thu, Dec 2, 2010 at 11:38 AM, Catein Catherine <>wrote:

> Dear All,
> I have done MM-GBSA analysis 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.............................................-30
> However, when I sum up all the TGBTOT from residue1 to residue500. I found
> the energy is about -30. I found the drug has binding eneryg 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) should be -30 (from residue 1
> to 500) plus -30 (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

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Thu Dec 02 2010 - 09:30:03 PST
Custom Search