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g_sasMain Table of Contents |
VERSION 3.1
Thu 28 Feb 2002
| VERSION 3.1 |
g_sas computes hydrophobic, hydrophilic and total solvent accessible surface area. As a side effect the Connolly surface can be generated as well in a pdb file where the nodes are represented as atoms and the vertices connecting the nearest nodes as CONECT records. The area can be plotted per atom and per residue as well (option -ao). In combination with the latter option an itp file can be generated (option -i) which can be used to restrain surface atoms.
By default, periodic boundary conditions are taken into account, this can be turned off using the -pbc option.
| option | filename | type | description |
|---|---|---|---|
| -f | traj.xtc | Input | Generic trajectory: xtc trr trj gro g96 pdb |
| -s | topol.tpr | Input | Generic run input: tpr tpb tpa |
| -o | area.xvg | Output | xvgr/xmgr file |
| -r | resarea.xvg | Output | xvgr/xmgr file |
| -q | connelly.pdb | Output, Opt. | Protein data bank file |
| -ao | atomarea.xvg | Output, Opt. | xvgr/xmgr file |
| -n | index.ndx | Input, Opt. | Index file |
| -i | surfat.itp | Output, Opt. | Include file for topology |
| option | type | default | description |
|---|---|---|---|
| -[no]h | bool | no | Print help info and quit |
| -[no]X | bool | no | Use dialog box GUI to edit command line options |
| -nice | int | 19 | Set the nicelevel |
| -b | time | -1 | First frame (ps) to read from trajectory |
| -e | time | -1 | Last frame (ps) to read from trajectory |
| -dt | time | -1 | Only use frame when t MOD dt = first time (ps) |
| -[no]w | bool | no | View output xvg, xpm, eps and pdb files |
| -solsize | real | 0.14 | Radius of the solvent probe (nm) |
| -ndots | int | 24 | Number of dots per sphere, more dots means more accuracy |
| -qmax | real | 0.2 | The maximum charge (e, absolute value) of a hydrophobic atom |
| -minarea | real | 0.5 | The minimum area (nm^2) to count an atom as a surface atom when writing a position restraint file (see help) |
| -skip | int | 1 | Do only every nth frame |
| -[no]pbc | bool | yes | Take periodicity into account |
| -[no]prot | bool | yes | Output the protein to the connelly pdb file too |
| -dgs | real | 0 | default value for solvation free energy per area (kJ/mol/nm^2) |