# MMPBSA Key Error: 'BDC' **URL:** \ **Category:** User discussions\ **Tags:** analysis-tools\ **Created:** [December 30, 2022, 4:27pm UTC](https://gromacs.bioexcel.eu/t/mmpbsa-key-error-bdc/5508 "2022-12-30T16:27:07Z")\ **Posts on this page:** 1\ **Page:** 1
**Author:** ![isilver](https://avatars.discourse-cdn.com/v4/letter/i/13edae/32.png) [@isilver](https://gromacs.bioexcel.eu/u/isilver)\ **Post date:** [December 30, 2022, 4:27pm UTC](https://gromacs.bioexcel.eu/t/mmpbsa-key-error-bdc/5508/1 "2022-12-30T16:27:07Z")
GROMACS version: GROMACS modification: Yes/No Here post your question Hi! I am trying to run an energy scoring of a simulation between two proteins using mmpbsa. I am trying to use decomposition, however, I receive a ‘BDC’ error, which I do not know what it is referring to or how to adjust it. Please advise! I have pasted the mmpbsa.in input file used below as well as the lines of code which appeared once the function was run. mmpbsa.in: Input file generated by gmx\_MMPBSA (v1.5.6) Be careful with the variables you modify, some can have severe consequences on the results you obtain. # General namelist variables &general sys\_name = “” # System name startframe = 1 # First frame to analyze endframe = 9999999 # Last frame to analyze interval = 1 # Number of frames between adjacent frames analyzed forcefields = “oldff/leaprc.ff99SB,leaprc.gaff” # Define the force field to build the Amber topology ions\_parameters = 1 # Define ions parameters to build the Amber topology PBRadii = 3 # Define PBRadii to build amber topology from GROMACS files temperature = 298.15 # Temperature qh\_entropy = 0 # Do quasi-harmonic calculation interaction\_entropy = 0 # Do Interaction Entropy calculation ie\_segment = 25 # Trajectory segment to calculate interaction entropy c2\_entropy = 0 # Do C2 Entropy calculation assign\_chainID = 0 # Assign chains ID exp\_ki = 0.0 # Experimental Ki in nM full\_traj = 0 # Print a full traj. AND the thread trajectories gmx\_path = “” # Force to use this path to get GROMACS executable keep\_files = 2 # How many files to keep after successful completion netcdf = 0 # Use NetCDF intermediate trajectories solvated\_trajectory = 1 # Define if it is necessary to cleanup the trajectories verbose = 1 # How many energy terms to print in the final output / # (AMBER) Generalized-Born namelist variables &gb igb = 5 # GB model to use intdiel = 1.0 # Internal dielectric constant for sander extdiel = 78.5 # External dielectric constant for sander saltcon = 0.0 # Salt concentration (M) surften = 0.0072 # Surface tension surfoff = 0.0 # Surface tension offset molsurf = 0 # Use Connelly surface (‘molsurf’ program) msoffset = 0.0 # Offset for molsurf calculation probe = 1.4 # Solvent probe radius for surface area calc ifqnt = 0 # Use QM on part of the system qm\_theory = “” # Semi-empirical QM theory to use qm\_residues = “” # Residues to treat with QM qmcharge\_com = 0 # Charge of QM region in complex qmcharge\_lig = 0 # Charge of QM region in ligand qmcharge\_rec = 0 # Charge of QM region in receptor qmcut = 9999.0 # Cutoff in the QM region scfconv = 1e-08 # Convergence criteria for the SCF calculation, in kcal/mol peptide\_corr = 0 # Apply MM correction to peptide linkages writepdb = 1 # Write a PDB file of the selected QM region verbosity = 0 # Controls the verbosity of QM/MM related output alpb = 0 # Use Analytical Linearized Poisson-Boltzmann (ALPB) arad\_method = 1 # Selected method to estimate the effective electrostatic size / Sample input file for decomposition analysis This input file is meant to show only that gmx\_MMPBSA works. Althought, we tried to used the input files as recommended in the Amber manual, some parameters have been changed to perform more expensive calculations in a reasonable amount of time. Feel free to change the parameters according to what is better for your system. sys\_name=“Decomposition”, startframe=1, endframe=10, forcefields=“leaprc.protein.ff14SB” / igb=5, saltcon=0.150, / #make sure to include at least one residue from both the receptor #and ligand in the print\_res mask of the &decomp section. #this requirement is automatically fulfilled when using the within keyword. #[Re: [AMBER] Is there any problem with this input file? from Bill Miller III on 2013-08-05 (Amber Archive Aug 2013)](http://archive.ambermd.org/201308/0075.html) &decomp idecomp=2, dec\_verbose=3, print\_res=“within 4” / LINES OF CODE AFTER FUNCTION WAS RUN: gmx\_MMPBSA -O -i mmpbsa.in -cs md\_0\_10.tpr -ci index.ndx -cg 21 22 -ct md\_0\_10.xtc -cp topol.top [INFO] Checking mmpbsa.in input file… [INFO] Checking mmpbsa.in input file…Done. [INFO] Checking external programs… [INFO] cpptraj found! Using /home/dovschulman/miniconda3/bin/cpptraj [INFO] tleap found! Using /home/dovschulman/miniconda3/bin/tleap [INFO] parmchk2 found! Using /home/dovschulman/miniconda3/bin/parmchk2 [INFO] sander found! Using /home/dovschulman/miniconda3/bin/sander [INFO] Using GROMACS version \> 5.x.x! [INFO] gmx found! Using /usr/bin/gmx [INFO] Checking external programs…Done. [INFO] Building AMBER topologies from GROMACS files… [INFO] Get PDB files from GROMACS structures files… [INFO] Making gmx\_MMPBSA index for complex… [INFO] Normal Complex: Saving group 21\_22 in \_GMXMMPBSA\_COM\_index.ndx file as \_GMXMMPBSA\_COM.pdb [INFO] No receptor structure file was defined. Using ST approach… [INFO] Using receptor structure from complex to generate AMBER topology [INFO] Normal Receptor: Saving group 21 in \_GMXMMPBSA\_COM\_index.ndx file as \_GMXMMPBSA\_REC.pdb [INFO] No ligand structure file was defined. Using ST approach… [INFO] Using ligand structure from complex to generate AMBER topology [INFO] Normal Ligand: Saving group 22 in \_GMXMMPBSA\_COM\_index.ndx file as \_GMXMMPBSA\_LIG.pdb [INFO] Checking the structures consistency… [INFO] [INFO] Using topology conversion. Setting radiopt = 0… [INFO] Building Normal Complex Amber topology… [INFO] Detected Amber/OPLS force field topology format… [WARNING] 5981 invalid DIHEDRAL\_PERIODICITY = 0 found in Complex topology… Setting DIHEDRAL\_PERIODICITY = 1 [INFO] Assigning PBRadii mbondi2 to Complex… [INFO] Writing Normal Complex AMBER topology… [INFO] No Receptor topology file was defined. Using ST approach… [INFO] Building AMBER Receptor topology from Complex… [INFO] Assigning PBRadii mbondi2 to Receptor… [INFO] Writing Normal Receptor AMBER topology… [INFO] No Ligand topology file was defined. Using ST approach… [INFO] Building AMBER Ligand topology from Complex… [INFO] Assigning PBRadii mbondi2 to Ligand… [INFO] Writing Normal Ligand AMBER topology… [INFO] Selecting residues by distance (4 Å) between receptor and ligand for decomposition analysis… [INFO] Selected 61 residues: L:A:LYS:1000 L:A:LEU:1001 L:A:VAL:1002 L:A:ARG:1003 L:A:LEU:1017 L:A:LYS:1018 L:A:ASN:1019 L:A:GLY:1020 L:A:THR:1021 L:A:VAL:1023 L:A:SER:1033 L:A:MET:1034 L:A:ASN:1035 L:A:HIS:1037 L:A:MET:1043 L:A:LEU:1045 L:A:LYS:1046 L:A:ARG:1048 L:A:VAL:1051 L:A:GLN:1052 L:A:LEU:1053 L:A:GLU:1054 L:A:THR:1055 L:A:LEU:1056 L:A:SER:1057 L:A:ILE:1058 L:A:ARG:1059 L:A:GLY:1060 L:A:ASN:1061 L:A:ASN:1062 R:B:ASN:28 R:B:TYR:58 R:B:PRO:59 R:B:ILE:61 R:B:SER:62 R:B:LEU:63 R:B:HIS:64 R:B:ALA:65 R:B:LEU:66 R:B:SER:67 R:B:ARG:68 R:B:ASP:69 R:B:TYR:79 R:B:MET:81 R:B:VAL:82 R:B:ASN:83 R:B:VAL:106 R:B:GLU:107 R:B:PRO:108 R:B:ILE:109 R:B:GLU:111 R:B:ARG:113 R:B:PHE:126 R:B:CYS:130 R:B:GLN:133 R:B:HIS:136 R:B:PRO:137 R:B:ASP:138 R:B:ASP:141 R:B:SER:144 R:B:ASP:145 [INFO] Cleaning normal complex trajectories… [INFO] Building AMBER topologies from GROMACS files… Done. [INFO] Loading and checking parameter files for compatibility… [INFO] Preparing trajectories for simulation… [INFO] 1001 frames were processed by cpptraj for use in calculation. [INFO] Running calculations on normal system… [INFO] Beginning GB calculations with /home/dovschulman/miniconda3/bin/sander [INFO] calculating complex contribution… [INFO] calculating receptor contribution… [INFO] calculating ligand contribution… [INFO] Parsing results to output files… [INFO] Timing: [INFO] Total GROMACS setup time: 0.003 hr. [INFO] Total AMBER setup time: 0.000 hr. [INFO] Creating trajectories with cpptraj: 0.002 hr. [INFO] Total calculation time: 2.267 hr. [INFO] Total GB calculation time: 2.267 hr. [INFO] Statistics calculation & output writing: 0.000 hr. [INFO] Total time taken: 2.272 hr. [INFO] Finalizing gmx\_MMPBSA: [ERROR] = 0; [WARNING] = 1 Check the gmx\_MMPBSA.log file for more details… [INFO] Thank you for using gmx\_MMPBSA. Please consider supporting gmx\_MMPBSA by citing our publication: Valdés-Tresanco, M.S., Valdés-Tresanco, M.E., Valiente, P.A. and Moreno E. gmx\_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS. J Chem Theory Comput., 2021, 17 (10):6281-6291. Epub 2021 Sep 29. PMID: 34586825. [https://pubs.acs.org/doi/10.1021/acs.jctc.1c00645](https://pubs.acs.org/doi/10.1021/acs.jctc.1c00645) Also consider citing MMPBSA.py: Miller III, B. R., McGee Jr., T. D., Swails, J. M. Homeyer, N. Gohlke, H. and Roitberg, A. E. MMPBSA.py: An Efficient Program for End-State Free Energy Calculations. J. Chem. Theory Comput., 2012, 8 (9) pp 3314-3321 [INFO] Opening gmx\_MMPBSA\_ana to analyze results… multiprocessing.pool.RemoteTraceback: “”" Traceback (most recent call last): File “/home/dovschulman/miniconda3/lib/python3.9/site-packages/pandas/core/indexes/base.py”, line 3621, in get\_loc return self.\_engine.get\_loc(casted\_key) File “pandas/\_libs/index.pyx”, line 136, in pandas.\_libs.index.IndexEngine.get\_loc File “pandas/\_libs/index.pyx”, line 163, in pandas.\_libs.index.IndexEngine.get\_loc File “pandas/\_libs/hashtable\_class\_helper.pxi”, line 5198, in pandas.\_libs.hashtable.PyObjectHashTable.get\_item File “pandas/\_libs/hashtable\_class\_helper.pxi”, line 5206, in pandas.\_libs.hashtable.PyObjectHashTable.get\_item KeyError: ‘BDC’ The above exception was the direct cause of the following exception: Traceback (most recent call last): File “/home/dovschulman/miniconda3/lib/python3.9/multiprocessing/pool.py”, line 125, in worker result = (True, func(\*args, \*\*kwds)) File “/home/dovschulman/miniconda3/lib/python3.9/site-packages/GMXMMPBSA/analyzer/dialogs.py”, line 585, in run\_process obj = obj\_method(\*\*v[‘args’]) if v[‘args’] else obj\_method() File “/home/dovschulman/miniconda3/lib/python3.9/site-packages/GMXMMPBSA/API.py”, line 810, in get\_ana\_data dict(data=decomp[level][level1][level2][level3], level=item\_lvl, File “/home/dovschulman/miniconda3/lib/python3.9/site-packages/pandas/core/frame.py”, line 3504, in **getitem** return self.\_getitem\_multilevel(key) File “/home/dovschulman/miniconda3/lib/python3.9/site-packages/pandas/core/frame.py”, line 3555, in \_getitem\_multilevel loc = self.columns.get\_loc(key) File “/home/dovschulman/miniconda3/lib/python3.9/site-packages/pandas/core/indexes/multi.py”, line 2869, in get\_loc loc = self.\_get\_level\_indexer(key, level=0) File “/home/dovschulman/miniconda3/lib/python3.9/site-packages/pandas/core/indexes/multi.py”, line 3222, in \_get\_level\_indexer idx = self.\_get\_loc\_single\_level\_index(level\_index, key) File “/home/dovschulman/miniconda3/lib/python3.9/site-packages/pandas/core/indexes/multi.py”, line 2802, in \_get\_loc\_single\_level\_index return level\_index.get\_loc(key) File “/home/dovschulman/miniconda3/lib/python3.9/site-packages/pandas/core/indexes/base.py”, line 3623, in get\_loc raise KeyError(key) from err KeyError: ‘BDC’ “”" The above exception was the direct cause of the following exception: Traceback (most recent call last): File “/home/dovschulman/miniconda3/lib/python3.9/site-packages/GMXMMPBSA/analyzer/dialogs.py”, line 598, in run for result in imap\_unordered\_it: File “/home/dovschulman/miniconda3/lib/python3.9/multiprocessing/pool.py”, line 870, in next raise value KeyError: ‘BDC’ [ERROR] Unable to start gmx\_MMPBSA\_ana… [INFO] Finalized…