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This is a very prelimary version of app for calculating the enthalpy and entropy of water molecules in protein.
Dr. Xianqiang Sun [email protected]
Supervised by Prof. Yaoquan Tu
Citation: Sun, X., H. Agren, and Y. Tu. 2014. 'Functional water molecules in rhodopsin activation', The Journal of Physical Chemistry B, 118: 10863-73. (website)
I am currently updating new version of this software and it will be release in the end of 2017.
a. Read the trajectory file ('.dcd' as file extension), with python script 'readDCDFile.py',you will get the file name 'distance.txt', which includes all the oxygen atom information and coordinates.
b. Cluster all the water oxygen coordinated in the 'distance.txt' file to obtain the centers. c. Optimizing the centers obtained in the last step to combine centers near each other. d. Read the center coordinates and save H2O coordinates according to each center. 'getH2OCoordidateAll.py' is used in this step, and the coordinates for H and O atoms were saved into 'WW_allCentre_H2O.txt'.
a. Using 'SW_TranEntr.py' to calculate the protein-water correlation entropy for each water molecule. The output file is saves in 'SW.dat'.
a. 'WW_trans.py' is used to calculate the translational entropy of each water molecules. The output file is saved in 'WW_Trans.dat'. b.'WW_orientation_R3.py' or 'WW_orientation_R5.py' can be used to save the entropy wo water-water orientational entropy of each water-water correlation. The output file is saved in 'water_Orien.txt'.
a. NAMDenergy in VMD is used to calculate the interaction energy of each system. 'energy_tcl_generation.py' is used to get the tcl file for namd energy calculation. PLS remind that include the namd directory and add -exe in each calculation.
b. Each interaction energy is extracted with 'extract_energy.py'.
Ps: ''water_Gww_R1.py' is used to calculate the five angle correlation of bulk water.