# Re: [AMBER] MMGBSA residue-wise decomposition

From: Jason Swails <jason.swails.gmail.com>
Date: Thu, 15 Mar 2012 10:10:50 -0400

On Thu, Mar 15, 2012 at 2:58 AM, Rajeswari A.
<rajeswari.biotech.gmail.com>wrote:

> Thank You Very much for your response Carlos Simmerling and Jason. Sorry
> for not providing my input and output files. Now i am providing that.*
>
> *I am Looking at the stability calculation and want to see the pairwise
> decomposition energy. I am using Amber11 with Amber tools 1.5.
>
> *Input for run 1*
> &general
> startframe=1, endframe=1000, interval=10,
> keep_files=1, netcdf=1,
> /
> &gb
> igb=5, saltcon=0.1
> /
> &decomp
> idecomp=3, dec_verbose=3,
> /
> *Input for Run 2:*
> &general
> startframe=1, endframe=1000, interval=10,
> keep_files=1, netcdf=1,
> /
> &gb
> igb=5, saltcon=0.1
> /
> &decomp
> idecomp=4, dec_verbose=0,
> /
> Except the idecomp others are same. input trajectories, topologies are
> same.
>
> to Internal.
> Pairwise Energy Decomposition Analysis (All units kcal/mol): Generalized
> Born solvent
>
> Complex:
> Total Energy Decomposition:
> Resid 1 | Resid 2 | Internal | van der Waals |
> Electrostatic | Polar Solvation | Non-Polar Solv. | TOTAL
>
> -----------------------------------------------------------------------------------------------------------------------------------------------------
> PRO 1 | PRO 1 | 0.000 +/- 0.000 | -0.411 +/- 0.086 | -8.171
> +/- 3.189 | -52.944 +/- 2.320 | 1.947 +/- 0.017 | -59.579 +/-
> 3.944
> PRO 1 | GLN 2 | 0.000 +/- 0.000 | -0.859 +/- 0.176 | -22.013
> +/- 1.614 | 0.313 +/- 1.000 | -0.314 +/- 0.021 | -22.873 +/-
> 1.907
> PRO 1 | ILE 3 | 0.000 +/- 0.000 | -0.497 +/- 0.197 | -0.349
> +/- 0.208 | 0.069 +/- 0.231 | -0.125 +/- 0.048 | -0.902 +/-
> 0.371
> PRO 1 | THR 4 | 0.000 +/- 0.000 | -0.022 +/- 0.007 | -0.141
> +/- 0.356 | 0.115 +/- 0.348 | 0.000 +/- 0.000 | -0.049 +/-
> 0.498
> etc..
>
> output for idecomp = 4: Pairwise decomposition adding 1-4 interactions
> added to EEL and VDW.
> Pairwise Energy Decomposition Analysis (All units kcal/mol): Generalized
> Born solvent
>
> Complex:
> Total Energy Decomposition:
> Resid 1 | Resid 2 | Internal | van der Waals |
> Electrostatic | Polar Solvation | Non-Polar Solv. | TOTAL
>
> -----------------------------------------------------------------------------------------------------------------------------------------------------
> PRO 1 | PRO 1 | 0.000 +/- 0.000 | 0.310 +/- 0.507 | 50.413
> +/- 1.787 | -52.079 +/- 2.211 | 1.946 +/- 0.015 | 0.590 +/-
> 2.888
> PRO 1 | GLN 2 | 0.000 +/- 0.000 | -0.450 +/- 0.274 | -8.293
> +/- 1.360 | 0.426 +/- 1.120 | -0.306 +/- 0.021 | -8.623 +/-
> 1.783
> PRO 1 | ILE 3 | 0.000 +/- 0.000 | -0.520 +/- 0.155 | -0.339
> +/- 0.169 | 0.083 +/- 0.187 | -0.129 +/- 0.037 | -0.905 +/-
> 0.298
> PRO 1 | THR 4 | 0.000 +/- 0.000 | -0.023 +/- 0.006 | -0.153
> +/- 0.379 | 0.126 +/- 0.371 | 0.000 +/- 0.000 | -0.050 +/-
> 0.531
>
> Jason sir, as u have mentioned "energy values between non-adjacent residues
> for idecomp=3 and idecomp=4 are identical here. but why it is different for
> adjacent residues and self (pro1 - pro 1)? shouldn't be the same too?
>

Adjacent residues may share dihedrals. As a result, the 1-4 interactions
will be included differently between idecomp=3 and idecomp=4. In one case,
the 1-4 interactions will be added to the internal potential terms, whereas
in the other case they will be added to the EEL (for 1-4 EEL) and VDW (for
1-4 VDW) terms. I would not expect the total energy to change, though,
barring the effect of the bug on the surface area calculation.

If they are different, I don't know why and someone more familiar with the
code or method would have to comment.

> I want to see the contribution of each residue to the overall stability.
> how should i go with my purpose? please suggest me please.
>

Have you thought about using idecomp=1 or 2?

All the best,
Jason

```--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Mar 15 2012 - 07:30:02 PDT
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