g_mmpbsa decompose
This scripts calculate final contribution energy of each residue from individual energetic terms obtained from the g_mmpbsa
Command summary
g_mmpbsa decompose [-h] [-m contrib_MM.dat] [-p contrib_pol.dat] [-a contrib_apol.dat] [-bs]
[-nbs 500] [-ct 999] [-o final_contrib_energy.dat]
[-ocsv final_contrib_energy.csv] [-om energyMapIn.dat]
Description
-h, --help
show this help message and exit
-m contrib_MM.dat, --molmech contrib_MM.dat
Molecular Mechanics energy contribution file obtained from g_mmpbsa.
-p contrib_pol.dat, --polar contrib_pol.dat
Polar solvation energy contribution file obtained from g_mmpbsa.
-a contrib_apol.dat, --apolar contrib_apol.dat
Non-Polar solvation energy contribution file obtained from g_mmpbsa.
-bs, --bootstrap
If given, Enable Boot Strap analysis to calculate standard error.
-nbs 500, --nbstep 500
Number of boot strap steps for average energy and standard error calculation.
-ct 999, --cutoff 999
Absolute Cutoff in kJ/mol - Residues with energy values above and below this value will be in output while other residues will be filtered out from the output. If its value is 999, all residues energy will be in output.
This option is useful to filter-out the residues that are either not contributing or contributing very less to the binding energy.
-o final_contrib_energy.dat, --output final_contrib_energy.dat
Final output file containing binding energy contribution of each residue.
-ocsv final_contrib_energy.csv, --outputCSV final_contrib_energy.csv
Final Decomposed Energy File im CSV format
-om energyMapIn.dat, --outmap energyMapIn.dat
It is input file for energy2bfac. It can be used with energy2bfac to map energy on structure for visualization.