(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