Output Files¶
The output file¶
This is how a typical output file ("FINAL_RESULTS_MMPBSA.dat" by default) looks like:
| 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)
|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%) | # (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
- = ΔEGB + ΔESURF
- = ΔGGAS + ΔGSOLV
- Binding free energy
ΔG binding = ΔTOTAL - TΔS
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 sum 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.
Temporary files¶
Warning
This section does not record all the temporary files that are currently generated.
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, every temporary file is described below. Note that not every temporary file is generated in every simulation. At the end of each description, the lowest value of the original “keep_files” variable that will retain this file will be shown in parentheses. Nevertheless, in the current version, all the files are retained for plotting purposes.
gmx_MMPBSA.log This file contains the output coming from gmx_MMPBSA.
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 thread with snapshots used for normal mode calcula- tions on the complex. (1)
_GMXMMPBSA_receptor_nm.mdcrd.# Trajectory file for each thread with snapshots used for normal mode calcula- tions on the receptor. (1)
_GMXMMPBSA_ligand_nm.mdcrd.# Trajectory file for each thread with snapshots used for normal mode calculations on the ligand. (1)
_GMXMMPBSA_ptrajentropy.in Input file that calculates the entropy via the quasi-harmonic approximation. This file is processed by ptraj. (2)
_GMXMMPBSA_avgcomplex.pdb PDB file containing the average positions of all complex conformations processed by
_GMXMMPBSA_cenptraj.in. It is used as the reference for the _GMXMMPBSA_ptrajentropy.in file above. (1)
_GMXMMPBSA_complex_entropy.out File into which the entropy results from _GMXMMPBSA_ptrajentropy.in analysis on the complex are dumped. (1)
_GMXMMPBSA_receptor_entropy.out Same as above, but for the receptor. (1)
_GMXMMPBSA_ligand_entropy.out Same as above, but for the ligand. (1)
_GMXMMPBSA_ptraj_entropy.out Output from running ptraj using _GMXMMPBSA_ptrajentropy.in. (1)
_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_complex_rism.out.# rism3d.snglpnt output file containing energy components of all complex snap- shots done with 3D-RISM (1)
_GMXMMPBSA_receptor_rism.out.# rism3d.snglpnt output file containing energy components of all receptor snap- shots done with 3D-RISM (1)
_GMXMMPBSA_ligand_rism.out.# rism3d.snglpnt output file containing energy components of all ligand snapshots done with 3D-RISM (1)
_GMXMMPBSA_pbsanderoutput.junk.# File containing the information dumped by sander.APBS to STDOUT. (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 com- plex 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 thread-specific files. For serial simulations, only #=0 files are created. For parallel, #=0 through NUM_PROC - 1 are created.
Created: February 8, 2021 07:10:13