Output Files¶
Project folder structure¶
The project structure in gmx_MMPBSA was not the best. The number of temporary files could be considerable depending on the type of calculation, reaching an absurd amount when many CPUs were used in parallel. A large number of files in a folder presents several problems. First, since it is generated in the same folder as the input files, it is hard to use them. Second, because of the large number, it becomes problematic to find a specific file. Lastly, folders with many files are not easy to handle for the GUI of operating systems due to indexing.
Therefore, we decided to make some changes in the working directory structure. Now, a folder called xBFReE_RESULTS is generated and then a folder is generated for each type of calculation, currently only mmpbsa, which contains all the temporary files. Since they are isolated, the _GMXMMPBSA_
prefix is no longer required.
.
├── com.pdb
├── com.tpr
├── com_traj.xtc
├── index.ndx
├── mmpbsa.in
├── topol.top
├── toppar
│ ├── forcefield.itp
│ ├── PROA.itp
│ ├── PROB.itp
│ ...
│ └── TP3.itp
├── xBFreE.log
├── FINAL_RESULTS_MMPBSA.dat
├── COMPACT_RESULTS_MMPBSA.xbfree
└── xBFreE_RESULTS
└── mmpbsa
├── COM_FIXED.pdb
├── COM_index.ndx
├── complex_gb.mdout.0
...
├── REC.pdb
├── REC.prmtop
└── restrt.0
Important
Note that the result files (FINAL_RESULTS_MMPBSA.dat
, DECOMP_RESULTS_MMPBSA.dat
and COMPACT_RESULTS_MMPBSA.xbfree
) are inside the working directory
The output file¶
FINAL_RESULTS_MMPBSA.dat
and DECOMP_RESULTS_MMPBSA.dat
are kept unchanged as plain text result files
COMPACT_RESULTS_MMPBSA.xbfree
is the file that will be used by default with xBFReE-Analyzer.
This is how a typical output file (FINAL_RESULTS_MMPBSA.dat
by default) looks like:
| Run on Tue Feb 8 22:31:58 2022 |
| +
|gmx_MMPBSA Version=v1.4.3+462.gf64aa73 based on MMPBSA.py v.16.0 |
|Complex Structure file com.tpr +
|Complex (AMBER) topology file COM.prmtop |
|Receptor (AMBER) topology file REC.prmtop |
|Ligand Structure file ligand.mol2 |
|Complex (AMBER) topology file LIG.prmtop |
|Initial trajectories COM_traj_0.xtc +
|
|Receptor mask ":1-240" +
|Ligand mask ":241" |
|Ligand residue name is "RAL" +
|
|Calculations performed using 16 complex frames +
|C2 Entropy Std. Dev. and Conf. Interv. (95%) have been obtained by bootstrapping |
|with number of re-samplings = 2000 |
| |
|Generalized Born ESURF calculated using 'LCPO' surface areas |
| |
|Using temperature = 300.00 K) |
|All units are reported in kcal/mol. |
| |
|SD - Sample standard deviation, SEM - Sample standard error of the mean |
|SD(Prop.), SEM(Prop.) - SD and SEM obtained with propagation of uncertainty formula |
|https://en.wikipedia.org/wiki/Propagation_of_uncertainty#Example_formulae +
------------------------------------------------------------------------------- +
------------------------------------------------------------------------------- |
ENTROPY RESULTS (C2 ENTROPY) |
Model σ(Int. Energy) C2 Value Std. Dev. Conf. Interv. (95%) |
------------------------------------------------------------------------------- |
gb 3.308 9.176 2.086 4.601-12.477 |
------------------------------------------------------------------------------- |
------------------------------------------------------------------------------- +
GENERALIZED BORN: |
Complex: +
Energy Component Average SD(Prop.) SD SEM(Prop.) SEM |
------------------------------------------------------------------------------- |
BOND 730.92 21.73 21.73 5.43 5.43 |
ANGLE 2022.96 27.54 27.54 6.89 6.89 |
DIHED 2631.46 15.99 15.99 4.00 4.00 |
VDWAALS -2035.53 14.81 14.81 3.70 3.70 |
EEL -16750.43 22.60 22.60 5.65 5.65 |
1-4 VDW 911.73 15.17 15.17 3.79 3.79 |
1-4 EEL 10292.96 23.03 23.03 5.76 5.76 |
EGB -3270.77 15.90 15.90 3.98 3.98 |
ESURF 96.07 0.58 0.58 0.15 0.15 |
|
GGAS -2195.93 54.56 33.37 13.64 8.34 |
GSOLV -3174.70 15.91 15.72 3.98 3.93 |
|
TOTAL -5370.63 56.84 31.88 14.21 7.97 +
Receptor: +
Energy Component Average SD(Prop.) SD SEM(Prop.) SEM |
------------------------------------------------------------------------------- |
BOND 719.57 21.28 21.28 5.32 5.32 |
ANGLE 1996.26 27.60 27.60 6.90 6.90 |
DIHED 2597.25 13.84 13.84 3.46 3.46 |
VDWAALS -1972.61 13.52 13.52 3.38 3.38 |
EEL -16735.20 22.33 22.33 5.58 5.58 |
1-4 VDW 895.00 14.81 14.81 3.70 3.70 |
1-4 EEL 10339.15 23.01 23.01 5.75 5.75 |
EGB -3288.63 16.59 16.59 4.15 4.15 |
ESURF 99.77 0.61 0.61 0.15 0.15 |
|
GGAS -2160.58 53.26 35.11 13.31 8.78 |
GSOLV -3188.86 16.60 16.39 4.15 4.10 |
|
TOTAL -5349.43 55.78 32.13 13.95 8.03 +
Ligand: +
Energy Component Average SD(Prop.) SD SEM(Prop.) SEM |
------------------------------------------------------------------------------- |
BOND 11.35 1.94 1.94 0.48 0.48 |
ANGLE 26.70 2.68 2.68 0.67 0.67 |
DIHED 34.21 3.59 3.59 0.90 0.90 |
VDWAALS -4.03 1.35 1.35 0.34 0.34 |
EEL 15.90 0.96 0.96 0.24 0.24 |
1-4 VDW 16.73 1.19 1.19 0.30 0.30 |
1-4 EEL -46.19 0.94 0.94 0.24 0.24 |
EGB -23.14 0.63 0.63 0.16 0.16 |
ESURF 4.52 0.02 0.02 0.00 0.00 |
|
GGAS 54.67 5.37 3.97 1.34 0.99 |
GSOLV -18.61 0.63 0.63 0.16 0.16 |
|
TOTAL 36.05 5.41 4.16 1.35 1.04 +
Delta (Complex - Receptor - Ligand): +
Energy Component Average SD(Prop.) SD SEM(Prop.) SEM |
------------------------------------------------------------------------------- |
ΔBOND 0.00 1.49 0.00 0.37 0.00 |
ΔANGLE 0.00 2.62 0.00 0.65 0.00 |
ΔDIHED -0.00 1.44 0.00 0.36 0.00 |
ΔVDWAALS -58.89 0.06 2.31 0.01 0.58 |
ΔEEL -31.13 0.69 3.04 0.17 0.76 |
Δ1-4 VDW 0.00 0.83 0.00 0.21 0.00 |
Δ1-4 EEL -0.00 0.92 0.00 0.23 0.00 |
ΔEGB 40.99 0.05 1.41 0.01 0.35 |
ΔESURF -8.22 0.01 0.09 0.00 0.02 |
|
ΔGGAS -90.02 0.69 3.31 0.17 0.83 |
ΔGSOLV 32.77 0.06 1.37 0.01 0.34 |
|
ΔTOTAL -57.25 0.69 2.55 0.17 0.64 +
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
Using C2 Entropy Approximation: |
ΔG binding = -48.0704 +/- 2.1972 |
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
The header of the output file will contain information about the calculation. It will also show the names of all files that were used in the calculation (topology files and coordinate file(s)). If the masks were not specified, it prints its best guess so that you can verify its accuracy, along with the residue name of the ligand (if it is only a single residue). After that, general information about methods, units, constants used is included. Entropy results are shown next in case any entropy approximation was used. Next, the energy and entropy contributions are broken up into their components as they are in sander
and nmode
or cpptraj
. The contributions are further broken for the complex, receptor and ligand into GGAS
and GSOLV
. GGAS
is the interaction energy and is obtained after adding the internal(bonded) components (BOND
+ ANGLE
+ DIHED
) and the non-bonded (VDWAALS
+ EEL
) components. For GSOLV
, the polar and non-polar contributions are EGB
(or EPB
) and ESURF
(or ENPOLAR + EDISPER
), respectively for GB
(or PB
) calculations. A single trajectory protocol does not produce any differences between bond lengths, angles, dihedrals or 1-4 interactions between the complex and receptor/ligand structures. Thus, when subtracted, they cancel completely. If not, these values are displayed and inconsistency warnings are printed. When this occurs, the results are generally useless. Of course, this does not hold for the multiple trajectory protocol as independent trajectories are used for the complex, receptor and ligand. Two approaches are used when calculating the standard deviation and the standard error of the mean. The SD
and SEM
values are calculated using a sample (array) of values. On the other hand, SD(Prop.)
and SEM(Prop.)
are obtained with the propagation of uncertainty formula for f = A - B. Check this thread for more details on MM/PB(GB)SA statistics.
This is how a typical decomposition output file (FINAL_DECOMP_MMPBSA.dat
by default) looks like:
|Run on Tue Mar 9 23:48:23 2021 |
|GB non-polar solvation energies calculated with gbsa=2 +
|idecomp = 2 Per-residue decomp adding 1-4 interactions to EEL and VDW. |
|Energy Decomposition Analysis (All units kcal/mol) Generalized Born solvent +
Complex: |
Total Energy Decomposition: |
Residue Internal van der Waals Electrostatic Polar Solvation Non-Polar Solv. TOTAL
Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean
LEU 40 22.06 3.40 0.82 -6.83 1.27 0.31 -32.53 0.81 0.20 -1.57 0.38 0.09 0.01 0.00 0.00 -18.86 3.27 0.79
THR 41 19.15 2.58 0.63 -3.64 1.06 0.26 -36.16 0.96 0.23 -3.58 0.37 0.09 0.23 0.02 0.00 -23.99 1.97 0.48
ALA 44 15.67 1.92 0.47 -5.42 0.72 0.18 -7.54 0.90 0.22 -2.36 0.33 0.08 0.00 0.00 0.00 0.35 2.42 0.59
RAL 241 72.32 3.91 0.95 -16.88 2.66 0.65 -46.00 1.94 0.47 -0.74 0.89 0.22 0.42 0.02 0.00 9.12 3.79 0.92
Sidechain Energy Decomposition: |
Residue Internal van der Waals Electrostatic Polar Solvation Non-Polar Solv. TOTAL
Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean
LEU 40 9.64 2.16 0.52 -4.15 0.92 0.22 -27.51 0.45 0.11 4.14 0.11 0.03 0.01 0.00 0.00 -17.88 2.48 0.60
THR 41 6.60 1.19 0.29 -1.62 0.70 0.17 -26.20 0.93 0.23 2.38 0.25 0.06 0.23 0.02 0.00 -18.61 1.11 0.27
ALA 44 2.94 1.08 0.26 -2.20 0.26 0.06 2.19 0.13 0.03 -0.31 0.04 0.01 0.00 0.00 0.00 2.63 1.25 0.30
RAL 241 72.32 3.91 0.95 -16.88 2.66 0.65 -46.00 1.94 0.47 -0.74 0.89 0.22 0.42 0.02 0.00 9.12 3.79 0.92
Backbone Energy Decomposition: |
Residue Internal van der Waals Electrostatic Polar Solvation Non-Polar Solv. TOTAL
Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean
LEU 40 12.42 2.04 0.49 -2.67 0.66 0.16 -5.03 0.80 0.19 -5.70 0.43 0.11 0.00 0.00 0.00 -0.98 1.72 0.42
THR 41 12.55 1.83 0.44 -2.02 0.71 0.17 -9.95 0.98 0.24 -5.96 0.34 0.08 0.00 0.00 0.00 -5.38 1.59 0.39
ALA 44 12.72 1.21 0.29 -3.22 0.73 0.18 -9.73 0.87 0.21 -2.05 0.33 0.08 0.00 0.00 0.00 -2.28 1.44 0.35
RAL 241 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Receptor: |
Total Energy Decomposition: |
Residue Internal van der Waals Electrostatic Polar Solvation Non-Polar Solv. TOTAL
Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean
LEU 40 22.06 3.40 0.82 -4.37 1.27 0.31 -32.08 0.79 0.19 -2.68 0.39 0.09 0.23 0.02 0.01 -16.84 3.30 0.80
THR 41 19.15 2.58 0.63 -1.55 1.04 0.25 -35.55 0.96 0.23 -4.84 0.33 0.08 0.52 0.02 0.00 -22.28 2.03 0.49
ALA 44 15.67 1.92 0.47 -3.91 0.72 0.17 -7.61 0.86 0.21 -2.02 0.35 0.08 0.21 0.02 0.00 2.33 2.36 0.57
Sidechain Energy Decomposition: |
Residue Internal van der Waals Electrostatic Polar Solvation Non-Polar Solv. TOTAL
Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean
LEU 40 9.64 2.16 0.52 -2.70 0.89 0.21 -27.27 0.44 0.11 3.89 0.09 0.02 0.20 0.02 0.01 -16.25 2.49 0.60
THR 41 6.60 1.19 0.29 -0.40 0.70 0.17 -25.86 0.88 0.21 1.62 0.21 0.05 0.49 0.02 0.00 -17.55 1.10 0.27
ALA 44 2.94 1.08 0.26 -1.33 0.18 0.04 2.24 0.12 0.03 -0.43 0.04 0.01 0.20 0.01 0.00 3.62 1.17 0.28
Backbone Energy Decomposition: |
Residue Internal van der Waals Electrostatic Polar Solvation Non-Polar Solv. TOTAL
Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean
LEU 40 12.42 2.04 0.49 -1.66 0.66 0.16 -4.81 0.81 0.20 -6.57 0.42 0.10 0.03 0.01 0.00 -0.59 1.69 0.41
THR 41 12.55 1.83 0.44 -1.15 0.72 0.17 -9.70 0.95 0.23 -6.46 0.34 0.08 0.02 0.01 0.00 -4.73 1.65 0.40
ALA 44 12.72 1.21 0.29 -2.59 0.71 0.17 -9.85 0.84 0.20 -1.58 0.35 0.08 0.01 0.01 0.00 -1.28 1.46 0.35
Ligand: |
Total Energy Decomposition: |
Residue Internal van der Waals Electrostatic Polar Solvation Non-Polar Solv. TOTAL
Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean
RAL 1 72.32 3.91 0.95 12.61 2.08 0.51 -30.28 0.65 0.16 -23.18 0.63 0.15 5.65 0.03 0.01 37.11 4.05 0.98
Sidechain Energy Decomposition: |
Residue Internal van der Waals Electrostatic Polar Solvation Non-Polar Solv. TOTAL
Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean
RAL 1 72.32 3.91 0.95 12.61 2.08 0.51 -30.28 0.65 0.16 -23.18 0.63 0.15 5.65 0.03 0.01 37.11 4.05 0.98
Backbone Energy Decomposition: |
Residue Internal van der Waals Electrostatic Polar Solvation Non-Polar Solv. TOTAL
Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean
RAL 1 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
DELTAS: |
Total Energy Decomposition: |
Residue Location Internal van der Waals Electrostatic Polar Solvation Non-Polar Solv. TOTAL
Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean
LEU 40 R LEU 40 0.00 0.00 0.00 -2.46 0.21 0.05 -0.45 0.13 0.03 1.11 0.18 0.04 -0.22 0.02 0.01 -2.02 0.23 0.06
THR 41 R THR 41 0.00 0.00 0.00 -2.09 0.15 0.04 -0.60 0.12 0.03 1.26 0.15 0.04 -0.28 0.02 0.00 -1.72 0.17 0.04
ALA 44 R ALA 44 0.00 0.00 0.00 -1.50 0.13 0.03 0.07 0.05 0.01 -0.34 0.04 0.01 -0.21 0.02 0.00 -1.98 0.17 0.04
RAL 241 L RAL 1 0.00 0.00 0.00 -29.49 1.14 0.28 -15.72 1.60 0.39 22.44 0.74 0.18 -5.22 0.04 0.01 -28.00 1.36 0.33
Sidechain Energy Decomposition: |
Residue Location Internal van der Waals Electrostatic Polar Solvation Non-Polar Solv. TOTAL
Avg. td. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean
LEU 40 R LEU 40 0.00 0.00 0.00 -1.45 0.17 0.04 -0.23 0.10 0.02 0.25 0.05 0.01 -0.19 0.02 0.01 -1.63 0.15 0.04
THR 41 R THR 41 0.00 0.00 0.00 -1.22 0.13 0.03 -0.34 0.12 0.03 0.76 0.15 0.04 -0.26 0.02 0.00 -1.06 0.13 0.03
ALA 44 R ALA 44 0.00 0.00 0.00 -0.87 0.15 0.04 -0.05 0.02 0.01 0.13 0.02 0.00 -0.19 0.01 0.00 -0.99 0.16 0.04
RAL 241 L RAL 1 0.00 0.00 0.00 -29.49 1.14 0.28 -15.72 1.60 0.39 22.44 0.74 0.18 -5.22 0.04 0.01 -28.00 1.36 0.33
Backbone Energy Decomposition: |
Residue Location Internal van der Waals Electrostatic Polar Solvation Non-Polar Solv. TOTAL
Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean Avg. Std. Dev. Std. Err. of Mean
LEU 40 R LEU 40 0.00 0.00 0.00 -1.01 0.08 0.02 -0.22 0.10 0.02 0.86 0.18 0.04 -0.03 0.01 0.00 -0.40 0.11 0.03
THR 41 R THR 41 0.00 0.00 0.00 -0.87 0.10 0.02 -0.26 0.06 0.02 0.50 0.04 0.01 -0.02 0.01 0.00 -0.66 0.16 0.04
ALA 44 R ALA 44 0.00 0.00 0.00 -0.63 0.06 0.01 0.12 0.04 0.01 -0.47 0.04 0.01 -0.01 0.01 0.00 -1.00 0.08 0.02
RAL 241 L RAL 1 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
The header of the output file will contain information about the calculation and parameters specified. Next, the TDC, SDC, and BDC data are shown for the complex, receptor and ligand, respectively. Finally, the delta energies are shown by terms for TDC, SDC, and BDC, respectively.
Temporary files¶
For gmx_MMPBSA users!
This section and the temporary files structure are different to gmx_MMPBSA.
If xbfree
does not finish successfully, several of these files may be helpful for diagnosing the problem. For that reason, every temporary file is described below. Note that not every temporary file is generated in every simulation.
xBFreE.log
This file contains the output coming fromxBFReE
.gb|pb|gbnsr6.mdin
Input file that controls the GB|PB|GBNSR6 calculation done in sander.(gb|pb|gbnsr6)_decomp_(com|rec|lig).mdin
Input file that controls the GB|PB|GBNSR6 decomp calculation done in sander.gb_qmmm_(com|rec|lig).mdin
Input file that controls the GB QM/MM calculation done in sander.(complex|receptor|ligand).mdcrd.#
Processed trajectory file(s).(complex|receptor|ligand).nc.#
Processed trajectory file(s) in the NetCDF format.dummy(complex|receptor|ligand).inpcrd
Dummy inpcrd file.(complex|receptor|ligand).pdb
Dummy PDB file(complex|receptor|ligand)_nm.mdcrd.#
Processed trajectory file(s) for normal mode calculations.ptrajentropy.in
Input file that calculates the entropy via the quasi-harmonic approximation. This file is processed byptraj
.avgcomplex.pdb
PDB file containing the average positions of all complex conformations processed bycenptraj.in.
It is used as the reference for theptrajentropy.in
file above.(complex|receptor|ligand)_entropy.out
File into which the entropy results fromptrajentropy.in
analysis are dumped.ptraj_entropy.out
Output from runningptraj
usingptrajentropy.in
.(complex|receptor|ligand)_(gb|pb|gbnsr6|rism).mdout.#
output file containing energy components of all snapshots done in GB|PB|GBNSR6|RISM.mutant_...
These files are analogs of the files described above, but instead refer to the mutant system of alanine scanning calculations.*out.#
These files are thread-specific files. For serial simulations, only #=0 files are created. For parallel, #=0 through NUM_PROC - 1 are created.