Output Files¶
Viewing wide output
Output tables and legacy examples are intentionally wide. On a narrow screen, scroll horizontally to view the complete columns and filenames.
The output file¶
Legacy output illustration
The following code block is retained as a historical v1.4.3-format illustration. It is not the complete output contract for the 1.7.0 release: current summaries can include Block SD and Block SEM, automatic per-frame CSV files, and provenance artifacts described below. Use a result generated by the 1.7.0 line, or the bundled examples, when checking exact columns and headers.
The historical example shows the default text output file (FINAL_RESULTS_MMPBSA.dat):
| Run on Tue Feb 8 22:31:58 2022 | # (1)
| +
|gmx_MMPBSA Version=v1.4.3+462.gf64aa73 based on MMPBSA.py v.16.0 | # (2)
|Complex Structure file com.tpr +
|Complex (AMBER) topology file COM.prmtop |
|Receptor (AMBER) topology file REC.prmtop | # (3)
|Ligand Structure file ligand.mol2 |
|Complex (AMBER) topology file LIG.prmtop |
|Initial trajectories COM_traj_0.xtc +
|
|Receptor mask ":1-240" + # (4)
|Ligand mask ":241" |
|Ligand residue name is "RAL" +
|
|Calculations performed using 16 complex frames + # (5)
|IE and C2 uncertainty diagnostics use deterministic nonoverlapping|
|trajectory blocks (block SD / SEM and percentile ranges) |
| |
|Generalized Born ESURF calculated using 'LCPO' surface areas |
| |
|Using temperature = 300.00 K |
|All units are reported in kcal/mol. |
| |
|SD - Population standard deviation of the frames (ddof=0), SEM - SD / sqrt(number of frames) |
|SD(Prop.), SEM(Prop.) - SD and SEM obtained with propagation of uncertainty formula |
|Block SD, Block SEM - sample SD and SEM of deterministic nonoverlapping block means |
|https://en.wikipedia.org/wiki/Propagation_of_uncertainty#Example_formulae +
------------------------------------------------------------------------------- +
------------------------------------------------------------------------------- |
ENTROPY RESULTS (C2 ENTROPY) |
Model σ(Int. Energy) C2 Value Block SD Block P2.5-P97.5 | # (6)
------------------------------------------------------------------------------- |
gb 3.308 9.176 2.086 4.601-12.477 |
------------------------------------------------------------------------------- |
------------------------------------------------------------------------------- +
GENERALIZED BORN: | # (7)
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 | # (8)
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 | # (9)
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 | # (10)
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): + # (11)
Energy Component Average SD(Prop.) SD SEM(Prop.) SEM |
------------------------------------------------------------------------------- |
ΔBOND 0.00 1.49 0.00 0.37 0.00 | # (12)
ΔANGLE 0.00 2.62 0.00 0.65 0.00 | # (13)
ΔDIHED -0.00 1.44 0.00 0.36 0.00 | # (14)
ΔVDWAALS -58.89 0.06 2.31 0.01 0.58 | # (15)
ΔEEL -31.13 0.69 3.04 0.17 0.76 | # (16)
Δ1-4 VDW 0.00 0.83 0.00 0.21 0.00 | # (17)
Δ1-4 EEL -0.00 0.92 0.00 0.23 0.00 | # (18)
ΔEGB 40.99 0.05 1.41 0.01 0.35 | # (19)
ΔESURF -8.22 0.01 0.09 0.00 0.02 | # (20)
|
ΔGGAS -90.02 0.69 3.31 0.17 0.83 | # (21)
ΔGSOLV 32.77 0.06 1.37 0.01 0.34 | # (22)
|
ΔTOTAL -57.25 0.69 2.55 0.17 0.64 + # (23)
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
Using C2 Entropy Approximation: |
ΔG binding = -48.0704 +/- 2.1972 | # (24)
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
- Date of running
- gmx_MMPBSA version used
- Input files used
- Receptor and ligand masks
- General description of the methods used and units
- Entropy results in case any entropy approximation was used
- Model used (GB in this case)
- Energy components (complex)
- Energy components (receptor)
- Energy components (ligand)
- Energy components (delta)
- Bond potential term
- Angle potential term
- Dihedral potential term
- Van der Waals contribution
- Electrostatic contribution
- Van der Waals 1-4 contribution
- Electrostatic 1-4 contribution
- Polar contribution to the solvation free energy
- Non-polar contribution to the solvation free energy
- = ΔBOND + ΔANGLE + ΔDIHED + ΔVDWAALS + ΔEEL + Δ1-4 VDW + Δ1-4 EEL (plus applicable method-specific terms)
- = ΔEGB + ΔESURF
- = ΔGGAS + ΔGSOLV
- Binding free energy
ΔG binding = ΔTOTAL + (−TΔS)
Use the printed[ -TΔS ]value as-is (it already includes the minus sign). Do not subtract that column again from ΔTOTAL.
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 gas-phase total for the applicable method. For ordinary AMBER calculations it is the sum of BOND, ANGLE, DIHED, VDWAALS, EEL, 1-4 VDW, and 1-4 EEL. CHARMM-based calculations can additionally include UB, IMP, and CMAP; QM/MMGBSA can additionally include ESCF. The exact displayed set is therefore method- and force-field-dependent. GGAS is not automatically an interaction energy for an isolated complex, and it should not be reduced to only bonded plus VDWAALS plus EEL when reconciling an absolute component total. 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 can cancel differences in bond, angle, dihedral, and 1-4 terms when matching topologies and frames are used; those terms still contribute to each component's GGAS and can remain nonzero in MT calculations. If ST terms do not cancel, inconsistency warnings are printed and the results require review. Independent trajectories in the multiple-trajectory protocol do not provide that cancellation automatically.
PB with eneopt = 1 (P3M), including NLPB
Amber reports EPB = 0 and folds reaction-field plus Coulomb into EEL. ΔGGAS / ΔGSOLV are then not a meaningful gas/solv split; use ΔTOTAL. Amber forces this bookkeeping for npbopt = 1. See eneopt and the NLPB example.
Two approaches are used when calculating the standard deviation, and the standard error of the mean. The SD and SEM values are calculated from the frame array using the population convention (ddof=0), with SEM = SD / sqrt(N). 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. Main energy and binding summaries also include adjacent Block SD and Block SEM columns. These are calculated from deterministic nonoverlapping block means; Block SEM is the preferred uncertainty when trajectory frames are correlated, while the legacy SD/SEM fields remain available for compatibility.
Frame ddof=0 vs block ddof=1
The Average column is unaffected by this choice: it is always the arithmetic mean of the frames (or of the selected block means for block diagnostics). Only the ± / SD / SEM columns differ by convention. Frame SD/SEM keep the historical MMPBSA.py population convention (ddof=0). Block SD uses the sample SD of the block means (ddof=1) because those means are treated as independent replicate estimates. Do not mix the two when comparing uncertainties across tools.
The block algorithm is deterministic. For a vector with N frames, candidate block sizes are max(2, N // d) for d in (16, 8, 4, 2, 1). The largest candidate that gives at least eight blocks is selected when possible; otherwise the largest candidate giving at least two blocks is used, or the largest candidate giving one block. The selected complete blocks are reshaped into block means, and any trailing frames that do not fill a complete block are excluded. Block SD is the sample SD (ddof=1) of those block means and Block SEM = Block SD / sqrt(number of blocks). With fewer than two blocks, block SD and block SEM are unavailable; primary uncertainty then falls back to the legacy population frame SEM. Block SEM summarizes the selected block means; it does not establish convergence or block independence, so a result with very few blocks is a weak uncertainty estimate. These sampling uncertainties also do not represent force-field, solvent-model, or other model error. For example, the 10-frame API fixture selects a block size of 5 and therefore has only 2 block means; that small block count is weak evidence for uncertainty and is not a convergence diagnostic.
Decomposition summaries report Avg., SD(Prop.), SD, SEM(Prop.), SEM, Block SD, and Block SEM for each component. The propagated columns are the uncertainty of the composed or subtracted quantity; the unqualified columns are calculated directly from the per-frame vector. Block statistics use the same deterministic nonoverlapping block-mean algorithm described above; Block SEM is the primary uncertainty for reported estimates when enough trajectory blocks are available. In the ASCII decomposition form, values are displayed as Avg. +/- Block SEM [SD(Prop.)/SD/SEM] / Block SD. Decomposition vector CSV files contain per-frame values only and are rounded to two decimals.
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 | # (1)!
|GB non-polar solvation energies calculated with gbsa=2 + # (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: | # (3)!
Total Energy Decomposition: | # (4)!
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: | # (5)!
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: | # (6)!
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: | # (7)!
Total Energy Decomposition: | # (8)!
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: | # (9)!
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: | # (10)!
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: | # (11)!
Total Energy Decomposition: | # (12)!
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: | # (13)!
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: | # (14)!
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: | # (15)!
Total Energy Decomposition: | # (16)!
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: | # (17)!
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: | # (18)!
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
- Date of running
- General description of the methods used and units
- Data for the complex
- Total Decomposition (TDC) by term for the complex (= Sidechain Energy Decomposition + Backbone Energy Decomposition)
- Sidechain Energy Decomposition (SDC) by term for the complex
- Backbone Energy Decomposition (BDC) by term for the complex
- Data for the receptor
- Total Decomposition (TDC) by term for the receptor (= Sidechain Energy Decomposition + Backbone Energy Decomposition)
- Sidechain Energy Decomposition (SDC) by term for the receptor
- Backbone Energy Decomposition (BDC) by term for the receptor
- Data for the ligand
- Total Decomposition (TDC) by term for the ligand (= Sidechain Energy Decomposition + Backbone Energy Decomposition)
- Sidechain Energy Decomposition (SDC) by term for the ligand
- Backbone Energy Decomposition (BDC) by term for the ligand
- Delta Energies
- Delta energy for the Total Decomposition (TDC) by term
- Delta energy for the Sidechain Energy Decomposition (SDC) by term
- Delta energy for the Backbone Energy Decomposition (BDC) by term
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.
GBNSR6 decomposition
With &gbnsr6, the Electrostatic column is sander Coulomb and Polar Solvation comes from GBNSR6 DGij. System totals still take EEL/EGB from GBNSR6. See GBNSR6 namelist.
Temporary files¶
Warning
This section lists the main generated files, not every implementation detail. Files marked as temporary are retained according to keep_files; preserve the compact result and provenance artifacts separately when a portable analysis bundle is required.
gmx_MMPBSA creates working files during the execution of the script beginning with the prefix _GMXMMPBSA_. If gmx_MMPBSA does not finish successfully, several of these files may be helpful in diagnosing the problem. For that reason, the common diagnostic files are described below. Not every file is generated in every simulation. At the end of each description, the lowest value of keep_files that retains the file is shown in parentheses where relevant. The compact result, text/CSV summaries, radius provenance, and automatic membrane diagnostics are retained separately when applicable.
Portable result and diagnostic artifacts¶
The files normally useful for moving or auditing a result are:
FINAL_RESULTS_MMPBSA.dat and FINAL_RESULTS_MMPBSA.csv The human-readable summary and per-frame energy table.
FINAL_DECOMP_MMPBSA.dat and its CSV counterpart Decomposition summary and per-frame decomposition data when decomposition is enabled.
_GMXMMPBSA_info Normalized inputs, file references, and serialized metadata used by the analyzer.
COMPACT_MMXSA_RESULTS.mmxsa The compact binary result consumed by gmx_MMPBSA_ana and the Python API. This is the portable compact filename; the obsolete _COMPACT_gmx_MMPBSA_RESULTS.mmxsa spelling should not be used.
GMXMMPBSA_radii.json Continuum-radius provenance written for every calculation. When radii_audit=1, GMXMMPBSA_radii_<component>.csv files add per-atom provenance.
GMXMMPBSA_membrane_parameters.csv and GMXMMPBSA_membrane_parameters.png Automatic membrane diagnostics, retained when membrane parameters are calculated.
gmx_MMPBSA_error_bundle_*.zip A collision-safe diagnostic archive created for failed calculations unless --no-error-bundle is supplied. Review its manifest and scientific-input contents before sharing it.
gmx_MMPBSA.log This file contains the output coming from gmx_MMPBSA. It is opened only after command-line parsing confirms that a calculation or output rewrite is starting, so --help and --version do not replace a previous calculation log. A real run starts a fresh log and replaces the existing file; run calculations in separate working directories when concurrent runs are needed. Log records use the compact [LEVEL] message format. Warning and error totals are counted from logging records, so multiline messages count once and formatting changes do not affect the totals. A nonfatal error is reported in the completion summary without changing the process exit status; fatal exceptions still terminate the run.
leap.log This file contains the output coming from tleap program.
_GMXMMPBSA_gb.mdin Input file that controls the GB calculation done in sander. (2)
_GMXMMPBSA_pb.mdin Input file that controls the PB calculation done in sander. (2)
_GMXMMPBSA_gb_decomp_com.mdin Input file that controls the GB decomp calculation for the complex done in sander. (2)
_GMXMMPBSA_gb_decomp_rec.mdin Input file that controls the GB decomp calculation for the receptor done in sander. (2)
_GMXMMPBSA_gb_decomp_lig.mdin Input file that controls the GB decomp calculation for the ligand done in sander. (2)
_GMXMMPBSA_pb_decomp_com.mdin Input file that controls the PB decomp calculation for the complex done in sander. (2)
_GMXMMPBSA_pb_decomp_rec.mdin Input file that controls the PB decomp calculation for the receptor done in sander. (2)
_GMXMMPBSA_pb_decomp_lig.mdin Input file that controls the PB decomp calculation for the ligand done in sander. (2)
_GMXMMPBSA_gb_qmmm_com.mdin Input file that controls the GB QM/MM calculation for the complex done in sander. (2)
_GMXMMPBSA_gb_qmmm_rec.mdin Input file that controls the GB QM/MM calculation for the receptor done in sander. (2)
_GMXMMPBSA_gb_qmmm_lig.mdin Input file that controls the GB QM/MM calculation for the ligand done in sander. (2)
_GMXMMPBSA_complex.mdcrd.# Trajectory file(s) that contains only those complex snapshots that will be processed by MMPBSA.py. (1)
_GMXMMPBSA_ligand.mdcrd.# Trajectory file(s) that contains only those ligand snapshots that will be processed by MMPBSA.py. (1)
_GMXMMPBSA_receptor.mdcrd.# Trajectory file(s) that contains only those receptor snapshots that will be processed by MMPBSA.py. (1)
_GMXMMPBSA_complex_nc.# Same as _GMXMMPBSA_complex.mdcrd.#, except in the NetCDF format. (1)
_GMXMMPBSA_receptor_nc.# Same as _GMXMMPBSA_receptor.mdcrd.#, except in the NetCDF format. (1)
_GMXMMPBSA_ligand_nc.# Same as _GMXMMPBSA_ligand.mdcrd.#, except in the NetCDF format. (1)
_GMXMMPBSA_dummycomplex.inpcrd Dummy inpcrd file generated by _GMXMMPBSA_complexinpcrd.in for use with imin=5 functionality in sander. (1)
_GMXMMPBSA_dummyreceptor.inpcrd Same as above, but for the receptor. (1)
_GMXMMPBSA_dummyligand.inpcrd Same as above, but for the ligand. (1)
_GMXMMPBSA_complex.pdb Dummy PDB file of the complex required to set molecule up in nab programs
_GMXMMPBSA_receptor.pdb Dummy PDB file of the receptor required to set molecule up in nab programs
_GMXMMPBSA_ligand.pdb Dummy PDB file of the ligand required to set molecule up in nab programs
_GMXMMPBSA_complex_nm.mdcrd.# Trajectory file(s) for each MPI rank with snapshots used for normal mode calculations on the complex. (1)
_GMXMMPBSA_receptor_nm.mdcrd.# Trajectory file for each MPI rank with snapshots used for normal mode calculations on the receptor. (1)
_GMXMMPBSA_ligand_nm.mdcrd.# Trajectory file for each MPI rank with snapshots used for normal mode calculations on the ligand. (1)
Legacy QH artifacts¶
The following names belong to historical quasi-harmonic workflows. They are retained here only to help identify files from older results; new QH calculations are not supported in 1.7.0:
_GMXMMPBSA_ptrajentropy.in Historical input file for the quasi-harmonic approximation, processed by ptraj. (legacy)
_GMXMMPBSA_avgcomplex.pdb Historical PDB file containing average complex positions. (legacy)
_GMXMMPBSA_cenptraj.in Historical centering input used with the files above. (legacy)
_GMXMMPBSA_complex_entropy.out Historical quasi-harmonic entropy output for the complex. (legacy)
_GMXMMPBSA_receptor_entropy.out Historical quasi-harmonic entropy output for the receptor. (legacy)
_GMXMMPBSA_ligand_entropy.out Historical quasi-harmonic entropy output for the ligand. (legacy)
_GMXMMPBSA_ptraj_entropy.out Historical output from ptraj using _GMXMMPBSA_ptrajentropy.in. (legacy)
_GMXMMPBSA_complex_gb.mdout.# sander output file containing energy components of all complex snapshots done in GB. (1)
_GMXMMPBSA_receptor_gb.mdout.# sander output file containing energy components of all receptor snapshots done in GB. ( 1)
_GMXMMPBSA_ligand_gb.mdout.# sander output file containing energy components of all ligand snapshots done in GB. (1)
_GMXMMPBSA_complex_pb.mdout.# sander output file containing energy components of all complex snapshots done in PB. (1)
_GMXMMPBSA_receptor_pb.mdout.# sander output file containing energy components of all receptor snapshots done in PB. ( 1)
_GMXMMPBSA_ligand_pb.mdout.# sander output file containing energy components of all ligand snapshots done in PB. (1)
_GMXMMPBSA_rism.mdin Sander input file generated for the 3D-RISM calculation. (1)
_GMXMMPBSA_complex_rism.mdout.# Sander output file containing energy components of all complex snapshots calculated with 3D-RISM. The corresponding receptor and ligand files use _receptor_rism.mdout.# and _ligand_rism.mdout.#. (1)
The # suffix identifies the wrapper MPI rank. These rank-specific files reflect frame distribution by gmx_MMPBSA; they should not be read as evidence that the RISM solver itself was launched as a separate rism3d.snglpnt process. (1)
_GMXMMPBSA_pbsanderoutput.junk.# Historical APBS solver output file. New calculations do not create this file. (1)
_GMXMMPBSA_ligand_nm.out.# Output file from mmpbsa_py_nabnmode that contains the entropy data for the ligand for all snapshots. (1)
_GMXMMPBSA_receptor_nm.out.# Output file from mmpbsa_py_nabnmode that contains the entropy data for the receptor for all snapshots. (1)
_GMXMMPBSA_complex_nm.out.# Output file from mmpbsa_py_nabnmode that contains the entropy data for the complex for all snapshots. (1)
_GMXMMPBSA_mutant_... These files are analogs of the files that only start with _GMXMMPBSA_ described above, but instead refer to the mutant system of alanine scanning calculations.
_GMXMMPBSA_*out.# These files are MPI-rank-specific files. For serial simulations, only #=0 files are created. For parallel, #=0 through NUM_PROC - 1 are created.
Compatibility of statistics and radius provenance¶
MMPBSA_API.get_binding() accepts legacy summaries containing Average, SD, and SEM, as well as summaries with Block SD and Block SEM. Missing block statistics are reported as NaN; frame-based uncertainties are not relabeled as block estimates. Reference-system plots adjust SD and SEM separately, including their block equivalents, using the existing correlated-difference convention.
For native AMBER, normal components use assignment_route=native_amber_topology_preserved. Mutated components use assignment_route=native_amber_mutant_inherited_ChRad: ParmEd reapplies the radius family inherited from the normal topology. Neither route applies the input PBRadii selection. An unchanged component reusing its normal topology retains the preserved route. GROMACS conversion continues to use assignment_route=parmed_ChRad with the requested PBRadii applied.
Created: February 8, 2021 07:10:13