SSTMap Solvation Structure and Thermodynamic Mapping

Understanding SSTMap Output

Both run_hsa and run_gist output several files, which are named after the prefix specfied under -o flag. In this post, we will describe these outputs.

HSA Output

Assuming that the output name was “testcase”, the following files are generated by run_hsa:

  • testcase_hsa_summary.txt: A text file containing a site-wise summary of HSA calculations, represented as an matrix, where is the number of hydration site. The columns of the matrix are described below.
ColumnQuantityDescription
0$$index$$Index (can be used as a selection handle in VMD)
1$$x$$x-coordinate of hydration site center
2$$y$$y-coordinate of hydration site center
3$$z$$z-coordinate of hydration site center
4$$N_{wat}$$Total number of waters in the site
5$$occupancy$$Occupnacy
6$$E_{sw}$$Average solute-water energy (kcal/mol)
7$$E_{sw,LJ}$$Average solute-water Lennard-Jones energy (kcal/mol)
8$$E_{sw,Elec}$$Average solute-water electrostatic energy (kcal/mol)
9$$E_{ww}$$Average water-water energy (kcal/mol)
10$$E_{ww,LJ}$$Average water-water Lennard-Jones energy (kcal/mol)
11$$E_{ww,Elec}$$Average water-water electrostatic energy (kcal/mol)
12$$E_{tot}$$Total average energy (kcal/mol)
13$$E_{ww,nbr}$$ Average water-water interaction energy per first shell neighbor (kcal/mol)
14$$TS_{sw,trans}$$Solute-water translational entropy (kcal/mol)
15$$TS_{sw,orient}$$Solute-water translational entropy (kcal/mol)
16$$TS_{tot}$$Total solute-water entropy (kcal/mol)
17$$N_{nbrs}$$ Average number of first shell neighbors
18$$N_{hb,ww}$$ Average water-water hydrogen bonds
19$$N_{hb,sw}$$ Average solute-water hydrogen bonds
20$$N_{hb,tot}$$Average total hydrogen bonds
21$$f_{hb,ww}$$ Average fraction of hydrogen-bonded neighbors
22$$f_{enc}$$ Average enclosure
23$$N_{acc,ww}$$ Number of water-water hydrogen bonds (donated)
24$$N_{don,ww}$$ Number of water-water hydrogen bonds (accepted)
25$$N_{acc,sw}$$ Number of solute-water hydrogen bonds (donated)
26$$N_{don,sw}$$ Number of solute-water hydrogen bonds (accepted)
27$$solute_acceptors$$Solute acceptors observed to H-bonds with water
28$$solute_donors$$Solute donors observed to H-bonds with water
  • testcase_hsa_data/: This is a directory containing text files for each hydration site, corresponding to quantities in columns 6:28, in the Table shown above. Within each file, every measurement corresponding of the quantity is recorded for the hydration site. These text files can be used to see the full distribution of a particular quatity for a particular site, which is valuable for statistical analysis and comparison between sites belonging to different systems.
  • clustercenterfile.pdb: This PDB file contains all of the hydration sites generated from clustering, where each site is represented by the geometric center of all waters observed in the site. The coordinates of the site center of cluster center are assigned to a dummy oxygen atom for visualization purposes.
  • cluster.num.pdb: A PDB file is generated for each site (num corresponds to site index), which contains the full set of water molecules present in the site during the simulation.
  • testcase_num_prob.pdb: This PDB file contains the most probable configuration of the site with the index num.
  • probcenters.pdb: This PDB file contains the most probable configurations of all sites within.

GIST Output

The run_gist programs generated the followig files after completion of a sussessful run.

  • testcase_gist_data.txt: A text file containing a voxel-wise summary of GIST calculations, represented as an matrix, where is the number of voxel. The columns of the matrix are described below.
ColumnQuantityDescription
0$$index$$Voxel index
1$$x$$x-coordinate of the voxel
2$$y$$y-coordinate of the voxel
3$$z$$z-coordinate of the voxel
4$$N_{wat}$$Total number of waters in the site
5$$g_O$$Number density of water oxygen atoms
6$$g_H$$Number density of water hydrogen atoms
7$$TS_{tr,dens}$$Density-weighted solute-water translational entropy (kcal/molA^3)
8$$TS_{tr,norm}$$Normalized solute-water translational entropy (kcal/mol)
9$$TS_{or,dens}$$Density-weighted solute-water orientational entropy (kcal/molA^3)
10$$TS_{or,norm}$$Normalized solute-water orientational entropy (kcal/mol)
11$$E_{sw,dens}$$Density-weighted solute-water energy (kcal/molA^3)
12$$E_{sw,norm}$$Normalized solute-water energy (kcal/mol)
13$$E_{ww,dens}$$Density-weighted water-water energy (kcal/molA^3)
14$$E_{ww,norm}$$Normalized water-water energy (kcal/mol)
15$$E_{ww,nbr,dens}$$Density-weighted water-water interaction energy per first shell neighbor (kcal/molA^3)
16$$E_{ww,nbr,norm}$$Normalized water-water interaction energy per first shell neighbor (kcal/mol)
17$$N_{nbr,dens}$$Density-weighted number of first shell neighbors
18$$N_{nbr,norm}$$Normalized number of first shell neighbors
19$$f_{hb,dens}$$Density-weighted number of H-bonded first shell neighbors
20$$f_{hb,norm}$$Normalized number of first shell neighbors
21$$f_{enc,dens}$$Density-weighted enclosure
22$$f_{enc,norm}$$Normalized enclosure
23$$N_{hb,sw,dens}$$Density-weighted number of solute-water H-bonds
24$$N_{hb,sw,norm}$$Normalized number of solute-water H-bonds
25$$N_{hb,ww,dens}$$Density-weighted number of water-water H-bonds
26$$N_{hb,ww,norm}$$Normalized number of water-water H-bonds
27$$N_{don,sw,dens}$$Density-weighted number of accepted solute-water H-bonds
28$$N_{don,sw,norm}$$Normalized number of accepted solute-water H-bonds
29$$N_{acc,sw,dens}$$Density-weighted number of donated solute-water H-bonds
30$$N_{acc,sw,norm}$$Normalized number of donated solute-water H-bonds
31$$N_{don,ww,dens}$$Density-weighted number of accepted water-water H-bonds
32$$N_{don,ww,norm}$$Normalized number of accepted water-water H-bonds
33$$N_{acc,ww,dens}$$Density-weighted number of donated water-water H-bonds
34$$N_{acc,ww,norm}$$Normalized number of donated water-water H-bonds
  • DX files: For each quantity in the above Table (from cloumn 7 to 34), a dx file is generated. The Data Explorer (or dx) format allows 3D visualization of volumetric data, contoured at specific values. These files can be used to visualize mapping of each quantity on to the solute surface. GIST data can be interpreted in the same way as described in the Amber GIST tutorial. In addition, GIST post-processing tools developed in this Lab (available here) can also be used to perform further analysis of GIST out from run_gist.