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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)
&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
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…