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CodeEntropy

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CodeEntropy tool with POSEIDON code integrated to form a complete and generally applicable set of tools for calculating entropy

See CodeEntropy’s documentation for more information.

To run

Requirements

  • Python > 3.9
  • gcc
  • g++

Install via

pip install CodeEntropy

Input

For supported format (AMBER NETCDF and GROMACS TRR) you will need to output the coordinates and forces to the same file.

See Format overview — MDAnalysis User Guide documentation

Command-line tool

A quick and easy way to get started is to use the command-line tool which you can run in bash by simply typing CodeEntropyPoseidon (Note: this doesn't work on Windows!!!)

For help

CodeEntropyPoseidon -h

Arguments

Arguments Description Default type
-f, --top_traj_file Path to Structure/topology file (AMBER PRMTOP or GROMACS TPR) followed by Trajectory file(s) (AMBER NETCDF or GROMACS TRR). You will need to output the coordinates and forces to the same file Require at least 2 file: a topology and a trajectory file list of str
-l, --selectString Selection string for CodeEntropy such as protein or resid, refer to MDAnalysis.select_atoms for more information. "all": select all atom in trajectory for CodeEntropy analysis for trajectory without solvent str
-b, --begin Start analysing the trajectory from this frame index. 0: From begining int
-e, --end Stop analysing the trajectory at this frame index -1: end of trajectory int
-d, --step Steps between frame 1 int
-k, --tempra Temperature for entropy calculation (K) 298.0 float
-t, --thread How many multiprocess to use. 1: for single core execution int
-o, --out Name of the file where the text format output will be written. outfile.out str
-v, --csvout Name of the file where the total entropy output will be written. outfile.csv str
-r, --resout Name of the file where the residue entropy output will be written. res_outfile.csv str
-m, --mout Name of the file where certain matrices will be written. None str
-n, --nmd Name of the file where VMD compatible NMD format files with mode information will be printed. None str
-a, --rotationalaxis The 3 atom name in each residue for rotational axis. ['C', 'CA', 'N'] : for protein list of str
-c, --cutShell Include cutoff shell analysis, add cutoff distance in angstrom. None : will ust the RAD Algorithm. See Higham, Jonathan, and Richard H Henchman. “Locally adaptive method to define coordination shell.” The Journal of chemical physics vol. 145,8 (2016): 084108. doi:10.1063/1.4961439 list of str
-p, --pureAtomNum Reference molecule resid for system of pure liquid. 1 int
-x, --excludedResnames Exclude a list of molecule names from nearest non-like analysis. None list of str
-w, --water Resname for water molecules. WAT list of str
-s, --solvent Include resname of solvent molecules (case-sensitive). None list of str
--wm Do entropy calculation at whole molecule level (The whole molecule is treated as one single bead.). Flag, activate when included Flag
--res Do entropy calculation at residue level (A residue as a whole represents a bead.). Flag, activate when included Flag
--uatom Do entropy calculation at united atom level (A heavy atom and its covalently bonded H-atoms for an united atom and represent a bead.). Flag, activate when included Flag
--topog Compute the topographical entropy using
  • 1 : pLogP method (will separate between backbone and side chain)
  • 2: Corr. pLogP method (will separate between backbone and side chain)
  • 3: Corr. pLogP after adaptive enumeration of states
 0: no topographical analysis int
--solwm Do water entropy calculation at residue level (The whole molecule is treated as one single bead.). Flag, activate when included Flag
--solres Do water entropy calculation at residue level (A residue as a whole represents a bead. Flag, activate when included Flag
--soluatom Do solution entropy calculation at united atom level (A heavy atom and its covalently bonded H-atoms for an united atom and represent a bead.). Flag, activate when included Flag
--solContact Do solute contact calculation. Flag, activate when included Flag

Example

You need to clone this repository to download example trajectories.

# example 1 DNA
CodeEntropyPoseidon -f "Example/data/md_A4_dna.tpr" "Example/data/md_A4_dna_xf.trr" -a "C5'" "C4'" "C3'" -l "all" -t 8 --wm --res --uatom --topog 3

# example 2 lysozyme in water
CodeEntropyPoseidon -f "Example/data/1AKI_prod_60.tpr" "Example/data/1AKI_prod_60.trr" -l "protein" -b 1 -e 30 -d 2 --wm --res --uatom --topog 1 --solwm --solres --soluatom --solContact

Units

The program assumes the following default unit

Qunatity Unit
Length Å
time ps
charge e
mass u
force kJ/(mol·Å)

Copyright

Copyright (c) 2022, DonaldChung-HK, CCPBioSim

Acknowledgements

Project based on the