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.
Project description
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
|
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
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