CodeEntropy 0.3.9

CodeEntropy tool with POSEIDON code integrated to form a complete and generally applicable set of tools for computing entropy of macromolecular systems from the forces sampled in a MD simulation.

CodeEntropy

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

• Computational Molecular Science Python Cookiecutter version 1.6.
• arghya90/CodeEntropy version 0.3
• jkalayan/PoseidonBeta