1g_sas(1) GROMACS suite, VERSION 4.5 g_sas(1)
2
6 g_sas - computes solvent accessible surface area
7 VERSION 4.5
9
11 g_sas -f traj.xtc -s topol.tpr -o area.xvg -or resarea.xvg -oa atom‐
12 area.xvg -tv volume.xvg -q connelly.pdb -n index.ndx -i surfat.itp
13 -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum
14 -probe real -ndots int -qmax real -[no]f_index -minarea real -[no]pbc
15 -[no]prot -dgs real
16
18 g_sas computes hydrophobic, hydrophilic and total solvent accessible
19 surface area. As a side effect the Connolly surface can be generated
20 as well in a pdb file where the nodes are represented as atoms and the
21 vertices connecting the nearest nodes as CONECT records. The program
22 will ask for a group for the surface calculation and a group for the
23 output. The calculation group should always consists of all the
24 non-solvent atoms in the system. The output group can be the whole or
25 part of the calculation group. The area can be plotted per residue and
26 atom as well (options -or and -oa). In combination with the latter
27 option an itp file can be generated (option -i) which can be used to
28 restrain surface atoms.
29 By default, periodic boundary conditions are taken into account, this
32 can be turned off using the -nopbc option.
33 With the -tv option the total volume and density of the molecule can
36 be computed. Please consider whether the normal probe radius is appro‐
37 priate in this case or whether you would rather use e.g. 0. It is good
38 to keep in mind that the results for volume and density are very
39 approximate, in e.g. ice Ih one can easily fit water molecules in the
40 pores which would yield too low volume, too high surface area and too
41 high density.
42
44 -f traj.xtc Input
45 Trajectory: xtc trr trj gro g96 pdb cpt
46 -s topol.tpr Input
48 Structure+mass(db): tpr tpb tpa gro g96 pdb
49 -o area.xvg Output
51 xvgr/xmgr file
52 -or resarea.xvg Output, Opt.
54 xvgr/xmgr file
55 -oa atomarea.xvg Output, Opt.
57 xvgr/xmgr file
58 -tv volume.xvg Output, Opt.
60 xvgr/xmgr file
61 -q connelly.pdb Output, Opt.
63 Protein data bank file
64 -n index.ndx Input, Opt.
66 Index file
67 -i surfat.itp Output, Opt.
69 Include file for topology
70
73 -[no]hno
74 Print help info and quit
75 -[no]versionno
77 Print version info and quit
78 -nice int 19
80 Set the nicelevel
81 -b time 0
83 First frame (ps) to read from trajectory
84 -e time 0
86 Last frame (ps) to read from trajectory
87 -dt time 0
89 Only use frame when t MOD dt = first time (ps)
90 -[no]wno
92 View output xvg, xpm, eps and pdb files
93 -xvg enum xmgrace
95 xvg plot formatting: xmgrace, xmgr or none
96 -probe real 0.14
98 Radius of the solvent probe (nm)
99 -ndots int 24
101 Number of dots per sphere, more dots means more accuracy
102 -qmax real 0.2
104 The maximum charge (e, absolute value) of a hydrophobic atom
105 -[no]f_indexno
107 Determine from a group in the index file what are the hydrophobic
108 atoms rather than from the charge
109 -minarea real 0.5
111 The minimum area (nm2) to count an atom as a surface atom when writing
112 a position restraint file (see help)
113 -[no]pbcyes
115 Take periodicity into account
116 -[no]protyes
118 Output the protein to the connelly pdb file too
119 -dgs real 0
121 default value for solvation free energy per area (kJ/mol/nm2)
122
125 gromacs(7)
126 More information about GROMACS is available at <http://www.gro‐
128 macs.org/>.
129 Thu 26 Aug 2010 g_sas(1)