The program is compiled from the Fortran source, connolly.f, and the documentation is contained within the source as comment lines. These lines are abstracted into the file connolly.doc. This summary is taken from the documentation and annotated further based on some simple applications of the program and a review of its use in the literature.
Topics covered:
Use and file structurevan der Waals radii for use with the program
USE:
connolly command-file radii-file structure-file
Command-file example (file1.dat):
- surface points per unit area
| - probe radius
| | -buried surface flag, nor=0, see below
| | | -output flag, see below
5.000 1.50 0 0
buried surface flag:
0 accessible (MS) surface
1 only buried surface calculated
2 both buried and unburied surface calculated (buried flagged by 1 in
last field of output)
output flag:
0 ASCII LONG FORMAT
1 BINARY LONG
2 ASCII SHORT
3 BINARY SHORT
radii-file example (file2.dat):
- atom type
| - radius
| |
0 0.00
1 1.53
2 1.53
3 1.53
4 1.54
structure-file example (test.inp = structure of crambin):
x, y and z coordinates -atom type
| | | | - surface request, see below
| | | | | - molecule number
| | | | | |
7.77820 4.31170 -3.34210 28 2 1
7.69820 2.99670 -2.62910 1 2 1
6.41620 2.96770 -1.83410 2 2 1
5.99920 4.03770 -1.37310 9 2 1
surface request:
0 ignore this atom
1 "roll over" this one, but don't generate surface
2 generate surface for this atom
molecule number:
defines groups of atoms to be used to generate surfaces,
buried or unburied (see buried surface flag of command-file)
If you set the probe radius to zero, the van der Waals surface (vdWS) is calculated for the radii given.If you add a water radius (nominally 1.4) to all of the atomic radii, then use a probe radius of 0, the program calculates the solvent accessible surface (SAS) as defined by Richards (1977).
If you set the probe radius to water (nominally 1.4), then the surface is the molecular surface (MS) defined by Connolly (or the "Contact + Reentrant" surface defined by Richards).
sort CONTACT REENTRANT -o MS-OUTsorts the two pieces together into the file "MS-OUT" in atom order.
For surface-by-atom calculations, you need the nearest atom (1st number of output each line) and the area associate with each dot (8th number in each line). For some calculations, solvation energy for example, you will also need the atom type for each atom from the input structure file. The form of the output file (long ASCII format) is as follows:
- closest "touching" atom | - next closest "touching" atom | | - 3rd touching atom if applicable | | | - number of touching atoms to probe sphere | | | | x, y and z of MS dot Area x, y and z of - flag | | | | | | | | surface normal | 0 = surface | | | | | | | | | | | | 1 = buried 103 65 0 2 1.495 -7.665 -0.570 0.169 0.504 -0.787 0.355 0 103 65 0 2 1.525 -8.268 -1.216 0.245 0.484 -0.385 0.786 0
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