table of contents
g_sas(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | g_sas(1) |
NAME¶
g_sas - computes solvent accessible surface areaSYNOPSIS¶
g_sas -f traj.xtc -s topol.tpr -o area.xvg -or resarea.xvg -oa atomarea.xvg -tv volume.xvg -q connelly.pdb -n index.ndx -i surfat.itp -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -probe real -ndots int -qmax real -[no]f_index -minarea real -[no]pbc -[no]prot -dgs realDESCRIPTION¶
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 program will ask for a group for the surface calculation and a group for the output. The calculation group should always consists of all the non-solvent atoms in the system. The output group can be the whole or part of the calculation group. The average and standard deviation of the area over the trajectory 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.FILES¶
-f traj.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt
Structure+mass(db): tpr tpb tpa gro g96 pdb
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
Protein data bank file
Index file
Include file for topology
OTHER OPTIONS¶
-[no]hnoPrint help info and quit
Print version info and quit
Set the nicelevel
First frame (ps) to read from trajectory
Last frame (ps) to read from trajectory
Only use frame when t MOD dt = first time (ps)
View output .xvg, .xpm, .eps and .pdb files
xvg plot formatting: xmgrace, xmgr or none
Radius of the solvent probe (nm)
Number of dots per sphere, more dots means more accuracy
The maximum charge (e, absolute value) of a hydrophobic atom
Determine from a group in the index file what are the hydrophobic atoms rather than from the charge
The minimum area (nm2) to count an atom as a surface atom when writing a position restraint file (see help)
Take periodicity into account
Output the protein to the Connelly .pdb file too
Default value for solvation free energy per area (kJ/mol/nm2)
SEE ALSO¶
gromacs(7)Mon 4 Apr 2011 |