ThermoWat is a program to find binding site water molecules and calculate thermodynamic quantities for these water molecules. At the moment, it will only calculate energies of the water molecules, the entropy calculation is not properly implemented. Therefore, its main use is to find binding site water molecules.

The program uses a clustering algorithm to find the water in the binding site. This algorithm is explain in Abel, R., Young, T., Farid, R., Berne, B. J., Friesner, R. A. (2008) J. Am. Chem. Soc., 130, 2817-2831. DOI: 10.1021/ja0771033. The program will superpose each snapshot from one or several MD simulations on a reference pdb-file and thereafter save away the coordinates of water molecules within a specific radius of the ligand in the reference pdb-file. After all the snapshots have been processed, the program will cluster the binding site water molecules.

The usage of the program is as follow


where is a textfile controlling the behaviour of the program.

The code is written in Fortran95 and located locally in /away/bio/Amber/Thermowat

Samuel Genheden, 2012

Control file

The control file contains values of variables determining the execution of thermowat. Each variable name starts with an ampersand (&) and the rows that follow the variable name sets the variable and associated variables. Currently, the following variables can be set:

Example file:

5433 5463
r1_mdcrd4 1 40


The program will write out the number of water molecules found in the binding site for each processed snapshot. At the end, it will write out a summary: the average and maximum number of water molecules found in the binding site. It will also write out the number of water sites found and the average occupancy of each site.

The program produces three output-files. These are explained below; in all cases it was assumed that the $outprefix was the to pre


For each found water site, the program will write the following information for each of the water molecules in that cluster. The last water molecule in each site is the central atom.


This is average information for each water site. The information that is given is

Is an xyz-file that contains the Cartesian coordinates of the oxygen atom for each of the water molecules that has been clustered into a site.