gmx-sasa(1)

1GMX-SASA(1)                         GROMACS                        GMX-SASA(1)
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NAME

6       gmx-sasa - Compute solvent accessible surface area
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SYNOPSIS

9          gmx sasa [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
10                   [-o [<.xvg>]] [-odg [<.xvg>]] [-or [<.xvg>]] [-oa [<.xvg>]]
11                   [-tv [<.xvg>]] [-q [<.pdb>]] [-b <time>] [-e <time>]
12                   [-dt <time>] [-tu <enum>] [-fgroup <selection>]
13                   [-xvg <enum>] [-[no]rmpbc] [-[no]pbc] [-sf <file>]
14                   [-selrpos <enum>] [-probe <real>] [-ndots <int>] [-[no]prot]
15                   [-dgs <real>] [-surface <selection>] [-output <selection>]
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DESCRIPTION

18       gmx  sasa computes solvent accessible surface areas.  See Eisenhaber F,
19       Lijnzaad P, Argos P, Sander C, & Scharf M (1995) J. Comput.  Chem.  16,
20       273-284  for  the algorithm used.  With -q, the Connolly surface can be
21       generated as well in a .pdb file where the  nodes  are  represented  as
22       atoms  and  the  edges  connecting the nearest nodes as CONECT records.
23       -odg allows for estimation of solvation  free  energies  from  per-atom
24       solvation energies per exposed surface area.
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26       The  program  requires  a  selection  for the surface calculation to be
27       specified with -surface. This should always consist of all  non-solvent
28       atoms  in  the system. The area of this group is always calculated. Op‐
29       tionally, -output can specify additional selections,  which  should  be
30       subsets  of  the  calculation  group.  The solvent-accessible areas for
31       these groups are also extracted from the full surface.
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33       The average and standard deviation of the area over the trajectory  can
34       be calculated per residue and atom (options -or and -oa).
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36       With the -tv option the total volume and density of the molecule can be
37       computed. With -pbc (the default), you  must  ensure  that  your  mole‐
38       cule/surface  group  is  not split across PBC.  Otherwise, you will get
39       non-sensical results.  Please also consider whether  the  normal  probe
40       radius  is  appropriate  in  this case or whether you would rather use,
41       e.g., 0. It is good to keep in mind that the  results  for  volume  and
42       density  are  very  approximate. For example, in ice Ih, one can easily
43       fit water molecules in the pores which would yield a volume that is too
44       low, and surface area and density that are both too high.
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OPTIONS

47       Options to specify input files:
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49       -f [<.xtc/.trr/...>] (traj.xtc) (Optional)
50              Input  trajectory  or  single configuration: xtc trr cpt gro g96
51              pdb tng
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53       -s [<.tpr/.gro/...>] (topol.tpr) (Optional)
54              Input structure: tpr gro g96 pdb brk ent
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56       -n [<.ndx>] (index.ndx) (Optional)
57              Extra index groups
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59       Options to specify output files:
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61       -o [<.xvg>] (area.xvg)
62              Total area as a function of time
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64       -odg [<.xvg>] (dgsolv.xvg) (Optional)
65              Estimated solvation free energy as a function of time
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67       -or [<.xvg>] (resarea.xvg) (Optional)
68              Average area per residue
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70       -oa [<.xvg>] (atomarea.xvg) (Optional)
71              Average area per atom
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73       -tv [<.xvg>] (volume.xvg) (Optional)
74              Total volume and density as a function of time
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76       -q [<.pdb>] (connolly.pdb) (Optional)
77              PDB file for Connolly surface
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79       Other options:
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81       -b <time> (0)
82              First frame (ps) to read from trajectory
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84       -e <time> (0)
85              Last frame (ps) to read from trajectory
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87       -dt <time> (0)
88              Only use frame if t MOD dt == first time (ps)
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90       -tu <enum> (ps)
91              Unit for time values: fs, ps, ns, us, ms, s
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93       -fgroup <selection>
94              Atoms stored in the trajectory file (if not set, assume first  N
95              atoms)
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97       -xvg <enum> (xmgrace)
98              Plot formatting: xmgrace, xmgr, none
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100       -[no]rmpbc (yes)
101              Make molecules whole for each frame
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103       -[no]pbc (yes)
104              Use periodic boundary conditions for distance calculation
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106       -sf <file>
107              Provide selections from files
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109       -selrpos <enum> (atom)
110              Selection  reference positions: atom, res_com, res_cog, mol_com,
111              mol_cog,    whole_res_com,     whole_res_cog,     whole_mol_com,
112              whole_mol_cog,    part_res_com,    part_res_cog,   part_mol_com,
113              part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
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115       -probe <real> (0.14)
116              Radius of the solvent probe (nm)
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118       -ndots <int> (24)
119              Number of dots per sphere, more dots means more accuracy
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121       -[no]prot (yes)
122              Output the protein to the Connolly .pdb file too
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124       -dgs <real> (0)
125              Default value for solvation free energy per area (kJ/mol/nm^2)
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127       -surface <selection>
128              Surface calculation selection
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130       -output <selection>
131              Output selection(s)
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COPYRIGHT

140       2022, GROMACS development team
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1452022.3                           Sep 02, 2022                      GMX-SASA(1)

NAME

SYNOPSIS

DESCRIPTION

OPTIONS

SEE ALSO

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