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7 Free Energies
 

(Note: These tutorials are meant to provide illustrative examples of how to use the AMBER software suite to carry out simulations that can be run on a simple workstation in a reasonable period of time. They do not necessarily provide the optimal choice of parameters or methods for the particular application area.)
Copyright McGee, Miller, and Swails 2009

Python Script MMPBSA.py

Dwight McGee, Bill Miller III, and Jason Swails

The important files for calculating the binding free energy using MMPBSA.py are the topology files and the mdcrd file (ras-raf_top_mdcrd.tgz)

Decomposing the free energy contributions to the binding free energy of Ras-Raf in a per-residue or pairwise per-residue basis (amber11 only!)

We will now perform free energy decomposition on the Ras-Raf system demonstrated in Section 3.1. Amber supports two types of decomposition: pairwise and per-residue. Per-residue decomposition calculates the energy contribution of single residues by summing its interactions over all residues in the system. Pairwise decomposition calculates the interaction energy between pairs of residues in the system. We will carry out examples of both types below. Note that obtaining DELTA contributions on a per-residue basis will ONLY work if MMPBSA.py correctly guesses your mask. You will have to manually add the residue cards to the input files if you input your own masks.

a) Per-residue free energy decomposition

To run decomposition, the &decomp namelist must be specified in the input file for MMPBSA.py. Furthermore, the variable idecomp must be specified (there is no default value). Failure to assign a value to this variable will result in the program terminating with an informative error message. There are 4 allowed values for idecomp, two of them for per-residue decomposition and the other two for pairwise decomposition. The values 1 and 2 result in a per-residue decomposition scheme. Selecting 1 will add the 1-4 non-bonded interaction energies (1-4 EEL and 1-4 VDW) to the internal potential terms. Selecting 2 will add the 1-4 EEL interaction energies to the electrostatic potential term and the 1-4 VDW interaction energies to the van der Waals potential term.

The following MMPBSA.py input file will be used to perform per-residue decomposition using both PB and GB implicit solvent models: (NOTE: PB non-polar solvation energies are currently not decomposable)

mmpbsa_per_res_decomp.in
Per-residue GB and PB decomposition
&general
   endframe=50, verbose=1,
/
&gb
  igb=5, saltcon=0.100,
/
&pb
  istrng=0.100,
/
&decomp
  idecomp=1, print_res="5; 30-40; 170-200"
  dec_verbose=1,
/

The input files for MMPBSA.py are designed to be similar to the setup of an mdin file used in the sander module of AMBER. The start of each namelist is designated by an ampersand (&) followed by the name of the namelist. Furthermore, a backslash (/) or '&end' can be used to end the namelist. For a complete list of all variables please see the Amber Manual. This input file is divided into four namelists: &general, &pb, &gb, and &decomp.. The &general namelist is designed to specify variables that are not specific to a particular part of the calculation, but to all parts. In this setup we have defined RAS to be the receptor and RAF to be the ligand. The 'endframe' variable sets what frame of the mdcrd to stop on. The '&gb' and '&pb' namelist markers let the script know to perform MM-GBSA and MM-PBSA calculations with the given values defined within those namelists. The 'verbose' variable allows the user to specify how much output is written to the output file while the 'dec_verbose' variable allows the user to specify how much output is written to the decomp output file.

$AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -do FINAL_DECOMP_MMPBSA.dat -sp ras-raf_solvated.prmtop -cp ras-raf.prmtop -rp ras.prmtop -lp raf.prmtop -y *.mdcrd

Note that this can be run in parallel using MMPBSA.py.MPI. See Section 3.4 for more details. This will run the script interactively and print the progress of the calculation to STDOUT and any errors or warnings to STDERR. Finally, timings will be printed once the calculation has completed showing the time taken during each step of the calculation.

Command-line arguments can be given with shell-recognized wildcards (i.e. * and ? for bash). For example, the '-y *.mdcrd' on the command line tells the script to read in all files in the working directory that end with '.mdcrd' and use them as the trajectories to be analyzed.

Here are all the output files created by this script: per_res_output.tgz.

The script creates three unsolvated mdcrd files (complex, receptor, and ligand) using ptraj that are the coordinates analyzed during the GB and PB calculations. The *.mdout files contain the energies for all frames specified. An average pdb file is created as an average structure for minimization if entropy calculations are performed. All files created by MMPBSA.py should begin with the prefix '_MMPBSA_' except for the final output files: FINAL_RESULTS_MMPBSA.dat and FINAL_DECOMP_MMPBSA.dat

FINAL_RESULTS_MMPBSA.dat
| Run on Thu May 20 14:55:43 EDT 2010

|Input file:
|--------------------------------------------------------------
|Per-residue GB and PB decomposition
|&general
|   endframe=50, verbose=1,
|/
|&gb
|  igb=5, saltcon=0.100,
|/
|&pb
|  istrng=0.100,
|/
|&decomp
|  idecomp=1, print_res="5; 30-40; 170-200"
|  dec_verbose=1,
|/
|--------------------------------------------------------------
|Complex topology file:           ras-raf.prmtop
|Receptor topology file:          ras.prmtop
|Ligand topology file:            raf.prmtop
|Initial mdcrd(s):                prod.mdcrd
|
|Best guess for receptor mask:   ":1-166"
|Best guess for  ligand  mask:   ":167-242"

|Calculations performed using 50 frames.
|Poisson Boltzmann calculations performed using internal PBSA solver in sander.
|
|All units are reported in kcal/mole.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------

GENERALIZED BORN:

Complex:
Energy Component            Average              Std. Dev.   Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS                  -1863.7944               16.9979              2.4039
EEL                     -17200.7297               75.1734             10.6311
EGB                      -2918.9628               65.1000              9.2065
ESURF                       92.2138                0.9782              0.1383

G gas                   -19064.5240               77.0712             10.8995
G solv                   -2826.7490               65.1073              9.2076

TOTAL                   -21891.2730               52.3724              7.4066


Receptor:
Energy Component            Average              Std. Dev.   Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS                  -1268.1888               14.0912              1.9928
EEL                     -11557.0773               70.9920             10.0398
EGB                      -2314.8693               56.2410              7.9537
ESURF                       64.4513                0.6128              0.0867

G gas                   -12825.2661               72.3770             10.2356
G solv                   -2250.4181               56.2443              7.9542

TOTAL                   -15075.6842               36.8322              5.2089


Ligand:
Energy Component            Average              Std. Dev.   Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS                   -529.3090                9.3251              1.3188
EEL                      -4684.4720               35.7816              5.0603
EGB                      -1587.3051               26.8494              3.7971
ESURF                       38.5992                0.5158              0.0730

G gas                    -5213.7811               36.9768              5.2293
G solv                   -1548.7058               26.8544              3.7978

TOTAL                    -6762.4869               26.1943              3.7044


Differences (Complex - Receptor - Ligand):
Energy Component            Average              Std. Dev.   Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS                    -66.2966                4.2321              0.5985
EEL                       -959.1803               34.5681              4.8887
EGB                        983.2116               33.0175              4.6694
ESURF                      -10.8367                0.3832              0.0542

DELTA G gas              -1025.4769               34.8262              4.9252
DELTA G solv               972.3749               33.0197              4.6697


 DELTA G binding =        -53.1020     +/-      6.8437                 0.9678
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------

POISSON BOLTZMANN:

Complex:
Energy Component            Average              Std. Dev.   Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS                  -1863.7944               16.9979              2.4039
EEL                     -17200.7297               75.1734             10.6311
EPB                      -3216.4587               65.8638              9.3146
ECAVITY                     67.8762                0.7739              0.1094

G gas                   -19064.5240               77.0712             10.8995
G solv                   -3148.5825               65.8684              9.3152

TOTAL                   -22213.1066               51.7402              7.3172


Receptor:
Energy Component            Average              Std. Dev.   Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS                  -1268.1888               14.0912              1.9928
EEL                     -11557.0773               70.9920             10.0398
EPB                      -2489.5955               55.9343              7.9103
ECAVITY                     47.1495                0.4689              0.0663

G gas                   -12825.2661               72.3770             10.2356
G solv                   -2442.4460               55.9363              7.9106

TOTAL                   -15267.7121               38.0243              5.3774


Ligand:
Energy Component            Average              Std. Dev.   Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS                   -529.3090                9.3251              1.3188
EEL                      -4684.4720               35.7816              5.0603
EPB                      -1673.2574               27.4055              3.8757
ECAVITY                     28.0328                0.4091              0.0579

G gas                    -5213.7811               36.9768              5.2293
G solv                   -1645.2246               27.4085              3.8761

TOTAL                    -6859.0057               24.7882              3.5056


Differences (Complex - Receptor - Ligand):
Energy Component            Average              Std. Dev.   Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS                    -66.2966                4.2321              0.5985
EEL                       -959.1803               34.5681              4.8887
EPB                        946.3942               34.1674              4.8320
ECAVITY                     -7.3062                0.2973              0.0420

DELTA G gas              -1025.4769               34.8262              4.9252
DELTA G solv               939.0881               34.1687              4.8322



 DELTA G binding =        -86.3888     +/-      8.1817                 1.1571
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------

WARNINGS:
igb=5 should be used with either mbondi2 or bondi pbradii set. Yours are modified Bondi radii (mbondi)
FINAL_DECOMP_MMPBSA.dat
| Run on Thu May 20 14:55:43 EDT 2010
idecomp = 1: Decomposition per-residue adding 1-4 interactions added to Internal.
Energy Decomposition Analysis (All units kcal/mol): Generalized Born solvent


DELTAS:
Total Energy Decomposition:
Residue |  Location |       Internal      |    van der Waals    |    Electrostatic    |   Polar Solvation   |   Non-Polar Solv.   |       TOTAL       
-------------------------------------------------------------------------------------------------------------------------------------------------------
LYS   5 | R LYS   5 |    0.000 +/-  4.870 |   -0.156 +/-  1.465 |   69.267 +/-  9.154 |  -67.061 +/-  9.601 |   -0.009 +/-  0.156 |    2.040 +/- 14.208
ASP  30 | R ASP  30 |    0.000 +/-  5.623 |   -0.065 +/-  0.961 |  -52.559 +/- 11.072 |   52.622 +/-  9.530 |    0.000 +/-  0.084 |   -0.003 +/- 15.684
GLU  31 | R GLU  31 |    0.000 +/-  5.174 |   -0.247 +/-  1.099 |  -79.946 +/- 10.550 |   80.630 +/-  9.693 |   -0.227 +/-  0.125 |    0.210 +/- 15.272
TYR  32 | R TYR  32 |    0.000 +/-  4.615 |   -0.290 +/-  1.515 |    0.639 +/-  4.431 |   -0.076 +/-  3.229 |   -0.012 +/-  0.175 |    0.261 +/-  7.327
ASP  33 | R ASP  33 |    0.000 +/-  4.464 |   -0.556 +/-  1.073 | -103.116 +/-  5.820 |  103.788 +/-  5.821 |   -0.459 +/-  0.094 |   -0.343 +/-  9.426
PRO  34 | R PRO  34 |    0.000 +/-  3.388 |   -1.829 +/-  0.869 |   -3.383 +/-  2.647 |    3.854 +/-  1.944 |   -0.308 +/-  0.130 |   -1.666 +/-  4.800
THR  35 | R THR  35 |    0.000 +/-  5.702 |   -1.829 +/-  1.049 |    0.376 +/-  4.365 |    0.947 +/-  2.028 |   -0.204 +/-  0.070 |   -0.709 +/-  7.536
ILE  36 | R ILE  36 |    0.000 +/-  4.650 |   -2.987 +/-  1.918 |    0.092 +/-  2.149 |    0.991 +/-  0.697 |   -0.377 +/-  0.072 |   -2.282 +/-  5.515
GLU  37 | R GLU  37 |    0.000 +/-  5.221 |   -1.627 +/-  1.388 | -126.728 +/-  6.441 |  120.528 +/-  4.686 |   -0.745 +/-  0.048 |   -8.573 +/-  9.624
ASP  38 | R ASP  38 |    0.000 +/-  3.750 |   -1.583 +/-  1.560 | -104.899 +/-  6.925 |   99.370 +/-  5.710 |   -0.254 +/-  0.037 |   -7.367 +/-  9.852
SER  39 | R SER  39 |    0.000 +/-  3.447 |   -2.184 +/-  1.086 |  -13.696 +/-  3.959 |    8.918 +/-  1.800 |   -0.504 +/-  0.035 |   -7.466 +/-  5.655
TYR  40 | R TYR  40 |    0.000 +/-  4.687 |   -4.403 +/-  1.682 |   -3.076 +/-  2.884 |    1.652 +/-  1.092 |   -0.366 +/-  0.042 |   -6.193 +/-  5.858
ARG 170 | L ARG   4 |    0.000 +/-  4.987 |   -0.094 +/-  1.646 |  -86.951 +/- 10.352 |   82.074 +/-  6.005 |   -0.147 +/-  0.073 |   -5.118 +/- 13.069
VAL 171 | L VAL   5 |    0.000 +/-  3.812 |   -0.183 +/-  1.390 |    2.128 +/-  2.460 |   -2.010 +/-  0.555 |    0.000 +/-  0.008 |   -0.065 +/-  4.778
PHE 172 | L PHE   6 |    0.000 +/-  4.289 |   -0.217 +/-  0.944 |    0.037 +/-  1.743 |    0.132 +/-  0.939 |    0.000 +/-  0.064 |   -0.048 +/-  4.818
LEU 173 | L LEU   7 |    0.000 +/-  4.907 |   -0.398 +/-  1.241 |   -0.940 +/-  3.050 |    1.683 +/-  1.446 |    0.000 +/-  0.022 |    0.345 +/-  6.084
PRO 174 | L PRO   8 |    0.000 +/-  3.433 |   -0.188 +/-  1.422 |    2.303 +/-  3.219 |   -2.589 +/-  1.289 |    0.000 +/-  0.051 |   -0.474 +/-  5.083
ASN 175 | L ASN   9 |    0.000 +/-  4.796 |   -1.671 +/-  1.017 |   -1.833 +/-  4.740 |    4.535 +/-  2.409 |   -0.354 +/-  0.119 |    0.678 +/-  7.233
LYS 176 | L LYS  10 |    0.000 +/-  4.403 |   -1.848 +/-  0.810 |  -33.879 +/-  7.269 |   36.798 +/-  6.704 |   -0.315 +/-  0.107 |    0.756 +/- 10.856
GLN 177 | L GLN  11 |    0.000 +/-  4.261 |   -3.791 +/-  1.560 |   -1.910 +/-  3.338 |    4.530 +/-  2.016 |   -0.359 +/-  0.050 |   -1.530 +/-  5.983
ARG 178 | L ARG  12 |    0.000 +/-  6.180 |   -2.462 +/-  1.321 |  -77.671 +/-  6.496 |   73.669 +/-  4.608 |   -0.386 +/-  0.076 |   -6.850 +/- 10.167
THR 179 | L THR  13 |    0.000 +/-  4.716 |   -1.277 +/-  1.200 |  -10.976 +/-  3.020 |    9.344 +/-  0.977 |   -0.158 +/-  0.031 |   -3.068 +/-  5.810
VAL 180 | L VAL  14 |    0.000 +/-  4.196 |   -3.837 +/-  1.389 |   -3.014 +/-  2.541 |    2.972 +/-  0.804 |   -0.501 +/-  0.041 |   -4.379 +/-  5.161
VAL 181 | L VAL  15 |    0.000 +/-  4.333 |   -1.791 +/-  1.119 |   -3.565 +/-  2.809 |    3.472 +/-  0.656 |   -0.155 +/-  0.055 |   -2.039 +/-  5.324
ASN 182 | L ASN  16 |    0.000 +/-  4.282 |   -1.978 +/-  0.859 |   -3.199 +/-  5.507 |    3.645 +/-  2.886 |   -0.369 +/-  0.085 |   -1.900 +/-  7.598
VAL 183 | L VAL  17 |    0.000 +/-  4.088 |   -0.187 +/-  1.149 |    1.057 +/-  4.557 |   -0.672 +/-  2.388 |    0.000 +/-  0.073 |    0.199 +/-  6.671
ARG 184 | L ARG  18 |    0.000 +/-  4.797 |   -0.183 +/-  1.450 |  -90.812 +/-  7.977 |   87.306 +/-  6.336 |   -0.335 +/-  0.109 |   -4.023 +/- 11.353
ASN 185 | L ASN  19 |    0.000 +/-  5.744 |   -0.018 +/-  0.966 |   -0.268 +/-  7.498 |    0.303 +/-  4.029 |    0.000 +/-  0.099 |    0.017 +/- 10.315
GLY 186 | L GLY  20 |    0.000 +/-  2.371 |   -0.008 +/-  0.701 |   -0.334 +/-  2.324 |    0.379 +/-  1.810 |    0.000 +/-  0.057 |    0.037 +/-  3.846
MET 187 | L MET  21 |    0.000 +/-  3.770 |   -0.156 +/-  1.254 |   -1.692 +/-  3.999 |    1.697 +/-  2.588 |   -0.031 +/-  0.089 |   -0.181 +/-  6.204
SER 188 | L SER  22 |    0.000 +/-  5.828 |   -0.013 +/-  1.008 |    2.808 +/-  4.910 |   -2.793 +/-  1.893 |    0.000 +/-  0.061 |    0.002 +/-  7.917
LEU 189 | L LEU  23 |    0.000 +/-  4.943 |   -0.021 +/-  1.312 |    1.683 +/-  2.195 |   -1.464 +/-  0.671 |    0.000 +/-  0.013 |    0.197 +/-  5.606
HIP 190 | L HIP  24 |    0.000 +/-  5.252 |   -0.024 +/-  1.131 |  -43.617 +/-  5.567 |   43.652 +/-  4.925 |    0.000 +/-  0.083 |    0.011 +/-  9.172
ASP 191 | L ASP  25 |    0.000 +/-  3.724 |   -0.058 +/-  0.723 |   62.413 +/-  8.165 |  -61.719 +/-  8.199 |    0.000 +/-  0.107 |    0.636 +/- 12.178
CYS 192 | L CYS  26 |    0.000 +/-  5.318 |   -0.098 +/-  1.398 |    1.937 +/-  3.894 |   -1.552 +/-  1.485 |    0.000 +/-  0.042 |    0.287 +/-  6.900
LEU 193 | L LEU  27 |    0.000 +/-  4.324 |   -0.108 +/-  1.390 |    0.884 +/-  2.119 |   -0.740 +/-  0.648 |    0.000 +/-  0.006 |    0.036 +/-  5.054

... cut off 250 lines

The beginning of the output file lists general details about the calculation. The rest of the output file includes all the average energies, standard deviations, and standard error of the mean for GB followed by PB. After each section, the ΔG of binding is given along with the error values. The meaning of the different terms in this file is as follows:

VDWAALS = van der Waals contribution from MM.
EEL = electrostatic energy.
EPB/EGB = the electrostatic contribution to the solvation free energy calculated by PB or GB respectively.
ESURF/ECAVITY/ENPOLAR = nonpolar contribution to the solvation free energy calculated by an empirical model.
DELTA G binding = final estimated binding free energy calculated from the terms above. (kcal/mol)

The FINAL_DECOMP_MMPBSA.dat output file contains information regarding the interaction of each residue with the rest of the system broken down into component parts: internal (potential terms consisting of bond, angle, dihedral, and 1-4 interactions for idecomp=1), van der Waals (VDW and 1-4 VDW for idecomp=2), electrostatic (EEL and 1-4 EEL for idecomp=2), polar solvation, and non-polar solvation. This file is broken down into several sections as described below:

The decomposition energies for each residue in the complex, receptor, ligand, and DELTA (defined by complex - receptor - ligand) are printed in their own section. Furthermore, each of these are further broken down into backbone, sidechain, and total contributions to their decomposition energies. "Backbone" is the interaction energy between the backbone atoms with every other atom in the system. "Sidechain" is the interaction energy between the sidechain atoms with every other atom in the system. "Total" is the interaction energy between every atom in the residue with every other atom in the system (and is thus the sum of the Backbone and Sidechain values for that residue). Each residue term is broken down into its component parts, described above, with the average value of the interaction +/- the standard deviation of that term. The DELTA section contains an extra column, called "Location", that lists where the specific residue in the complex is found ('R' for receptor, 'L' for ligand). The variable dec_verbose controls how much is printed to the decomp output file (see the manual for details).

b) Pairwise per-residue free energy decomposition

NOTE: In our experience, pairwise decomposition analysis done with the PB implicit solvent model takes very long to accomplish. The below analysis, of 50 frames using both GB and PB, took 61 hours on 9 processors (9 separate, 32-bit, single-core 2.8 GHz Xeon processors). The GB analysis took 3 minutes, so if you choose to do PB pairwise decomposition, be prepared for a lengthy simulation time.

In this section, we will modify the input file to perform pairwise per-residue energy decomposition. This will be mostly the same as the per-residue section above with slight differences. The pairwise decomposition input file is shown below:

mmpbsa_pairwise_decomp.in
Pairwise GB and PB decomposition
&general
   endframe=50, verbose=1,
/
&gb
  igb=5, saltcon=0.100,
/
&pb
  istrng=0.100,
/
&decomp
  idecomp=1, print_res="5; 30-40; 170-200"
  dec_verbose=0,
/

The same command is used to start MMPBSA.py as was used for per-residue decomposition. However, more care must be used in defining print_res in the &decomp namelist for pairwise decomposition. The number of terms that need to be evaluated for pairwise decomposition scales as n2, where n is the number of residues specified by print_res. By default, print_res corresponds to every residue in the complex, which for Ras-Raf will create a decomp output file around 65 MB (over 450,000 lines). Moreover, the mdout files created by sander will also be very large (several GB depending on how many frames and pairs are analyzed), and the memory/time requirements for the parser become substantial (i.e. it may take several minutes just to parse the output). The pairs calculated correspond to the residues specified in print_res with each other residue specified in print_res. See the manual for description of print_res syntax.

Part of the output file is shown below:

FINAL_DECOMP_MMPBSA.dat
| Run on Sun May 23 05:36:28 EDT 2010
idecomp = 3: Pairwise decomposition adding 1-4 interactions added to Internal.
Pairwise Energy Decomposition Analysis (All units kcal/mol): Generalized Born solvent


DELTAS:
Total Energy Decomposition:
Resid 1 | Resid 2 |       Internal      |    van der Waals    |    Electrostatic    |   Polar Solvation   |   Non-Polar Solv.   |       TOTAL
-----------------------------------------------------------------------------------------------------------------------------------------------------
LYS   5 | LYS   5 |    0.000 +/-  0.000 |    0.000 +/-  1.075 |    0.000 +/-  3.408 |    1.601 +/-  7.229 |    0.000 +/-  0.051 |    1.601 +/-  8.064
LYS   5 | ASP  30 |    0.000 +/-  0.000 |    0.000 +/-  0.000 |    0.000 +/-  0.341 |   -0.000 +/-  0.339 |    0.000 +/-  0.000 |   -0.000 +/-  0.480
LYS   5 | GLU  31 |    0.000 +/-  0.000 |    0.000 +/-  0.000 |    0.000 +/-  0.350 |    0.000 +/-  0.348 |    0.000 +/-  0.000 |    0.000 +/-  0.494
LYS   5 | TYR  32 |    0.000 +/-  0.000 |    0.000 +/-  0.001 |    0.000 +/-  0.071 |    0.000 +/-  0.070 |    0.000 +/-  0.000 |    0.000 +/-  0.099
LYS   5 | ASP  33 |    0.000 +/-  0.000 |    0.000 +/-  0.000 |    0.000 +/-  0.434 |    0.000 +/-  0.431 |    0.000 +/-  0.000 |    0.000 +/-  0.612
LYS   5 | PRO  34 |    0.000 +/-  0.000 |    0.000 +/-  0.000 |    0.000 +/-  0.064 |    0.000 +/-  0.064 |    0.000 +/-  0.000 |    0.000 +/-  0.090
LYS   5 | THR  35 |    0.000 +/-  0.000 |    0.000 +/-  0.000 |    0.000 +/-  0.189 |    0.008 +/-  0.183 |    0.000 +/-  0.000 |    0.008 +/-  0.262
LYS   5 | ILE  36 |    0.000 +/-  0.000 |    0.000 +/-  0.001 |    0.000 +/-  0.120 |    0.021 +/-  0.130 |    0.000 +/-  0.000 |    0.021 +/-  0.177

... cut 1800 lines

ARG 200 | LEU 197 |    0.000 +/-  0.000 |    0.000 +/-  0.423 |    0.000 +/-  0.779 |   -0.226 +/-  0.442 |    0.000 +/-  0.022 |   -0.226 +/-  0.991
ARG 200 | LYS 198 |    0.000 +/-  0.000 |    0.000 +/-  0.284 |    0.000 +/-  0.793 |    0.237 +/-  0.572 |    0.000 +/-  0.011 |    0.237 +/-  1.018
ARG 200 | VAL 199 |    0.000 +/-  0.000 |    0.000 +/-  0.291 |    0.000 +/-  0.832 |    1.460 +/-  0.587 |    0.000 +/-  0.019 |    1.460 +/-  1.059
ARG 200 | ARG 200 |    0.000 +/-  0.000 |    0.000 +/-  0.562 |    0.000 +/-  3.888 |   14.394 +/-  2.388 |   -0.000 +/-  0.035 |   14.394 +/-  4.598
idecomp = 3: Pairwise decomposition adding 1-4 interactions added to Internal.
Pairwise Energy Decomposition Analysis (All units kcal/mol): Poisson Boltzmann solvent


DELTAS:
Total Energy Decomposition:
Resid 1 | Resid 2 |       Internal      |    van der Waals    |    Electrostatic    |   Polar Solvation   |   Non-Polar Solv.   |       TOTAL
-----------------------------------------------------------------------------------------------------------------------------------------------------
LYS   5 | LYS   5 |    0.000 +/-  0.000 |    0.000 +/-  1.075 |    0.000 +/-  3.408 |    0.670 +/-  7.128 |    0.000 +/-  0.000 |    0.670 +/-  7.974
LYS   5 | ASP  30 |    0.000 +/-  0.000 |    0.000 +/-  0.000 |    0.000 +/-  0.341 |    0.007 +/-  0.334 |    0.000 +/-  0.000 |    0.007 +/-  0.477
LYS   5 | GLU  31 |    0.000 +/-  0.000 |    0.000 +/-  0.000 |    0.000 +/-  0.350 |    0.009 +/-  0.344 |    0.000 +/-  0.000 |    0.009 +/-  0.491
LYS   5 | TYR  32 |    0.000 +/-  0.000 |    0.000 +/-  0.001 |    0.000 +/-  0.071 |    0.002 +/-  0.069 |    0.000 +/-  0.000 |    0.002 +/-  0.098
LYS   5 | ASP  33 |    0.000 +/-  0.000 |    0.000 +/-  0.000 |    0.000 +/-  0.434 |    0.007 +/-  0.423 |    0.000 +/-  0.000 |    0.007 +/-  0.606
LYS   5 | PRO  34 |    0.000 +/-  0.000 |    0.000 +/-  0.000 |    0.000 +/-  0.064 |   -0.000 +/-  0.063 |    0.000 +/-  0.000 |   -0.000 +/-  0.090
LYS   5 | THR  35 |    0.000 +/-  0.000 |    0.000 +/-  0.000 |    0.000 +/-  0.189 |    0.024 +/-  0.175 |    0.000 +/-  0.000 |    0.024 +/-  0.257
LYS   5 | ILE  36 |    0.000 +/-  0.000 |    0.000 +/-  0.001 |    0.000 +/-  0.120 |    0.009 +/-  0.102 |    0.000 +/-  0.000 |    0.009 +/-  0.158
LYS   5 | GLU  37 |    0.000 +/-  0.000 |    0.000 +/-  0.008 |    0.000 +/-  1.649 |   -0.223 +/-  1.624 |    0.000 +/-  0.000 |   -0.223 +/-  2.315
LYS   5 | ASP  38 |    0.000 +/-  0.000 |    0.000 +/-  0.009 |    0.000 +/-  1.802 |   -0.191 +/-  1.383 |    0.000 +/-  0.000 |   -0.191 +/-  2.272

... cut 1800 lines

Note that the FINAL_RESULTS_MMPBSA.dat will be exactly the same as the one for the per-residue decomposition, since the energy decomposition scheme does not affect the total values. Thus, to avoid redundancy that file is omitted here.


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(Note: These tutorials are meant to provide illustrative examples of how to use the AMBER software suite to carry out simulations that can be run on a simple workstation in a reasonable period of time. They do not necessarily provide the optimal choice of parameters or methods for the particular application area.)
Copyright McGee, Miller, and Swails 2009