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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.

WDIR structure for xbfree gmx_MMPBSA
.
├── 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:

FINAL_RESULTS_MMPBSA.dat
| 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:

FINAL_DECOMP_MMPBSA.dat
|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 from xBFReE.
  • 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 by ptraj.
  • avgcomplex.pdb PDB file containing the average positions of all complex conformations processed by
  • cenptraj.in. It is used as the reference for the ptrajentropy.in file above.
  • (complex|receptor|ligand)_entropy.out File into which the entropy results from ptrajentropy.in analysis are dumped.
  • ptraj_entropy.out Output from running ptraj using ptrajentropy.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.

1 year ago2023-07-17 1 year ago2023-05-27