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g_sasMain Table of Contents |
VERSION 3.2.0
Sun 25 Jan 2004
| VERSION 3.2.0 |
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 residue and atom as well (options -or and -oa). 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 xml |
| -o | area.xvg | Output | xvgr/xmgr file |
| -or | resarea.xvg | Output, Opt. | xvgr/xmgr file |
| -oa | atomarea.xvg | Output, Opt. | xvgr/xmgr file |
| -q | connelly.pdb | Output, Opt. | Protein data bank 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 |
| -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 |
| -[no]f_index | bool | no | Determine from a group in the index file what are the hydrophobic atoms rather than from the charge |
| -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) |
| -[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) |