g_sas_d (1) - Linux Manuals

g_sas_d: computes solvent accessible surface area


g_sas - computes solvent accessible surface area



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 -nice int -b time -e time -dt time -[no]w -[no]xvgr -probe real -ndots int -qmax real -[no]f_index -minarea real -[no]pbc -[no]prot -dgs real


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 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 -nopbc option.

With the -tv option the total volume and density of the molecule can be computed. Please consider whether the normal probe radius is appropriate in this case or whether you would rather use e.g. 0. It is good to keep in mind that the results for volume and density are very approximate, in e.g. ice Ih one can easily fit water molecules in the pores which would yield too low volume, too high surface area and too high density.


-f traj.xtc Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

-s topol.tpr Input
 Run input file: tpr tpb tpa 

-o area.xvg Output
 xvgr/xmgr file 

-or resarea.xvg Output, Opt.
 xvgr/xmgr file 

-oa atomarea.xvg Output, Opt.
 xvgr/xmgr file 

-tv volume.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 


 Print help info and quit

-nice int 19
 Set the nicelevel

-b time 0
 First frame (ps) to read from trajectory

-e time 0
 Last frame (ps) to read from trajectory

-dt time 0
 Only use frame when t MOD dt first time (ps)

 View output xvg, xpm, eps and pdb files

 Add specific codes (legends etc.) in the output xvg files for the xmgrace program

-probe 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

 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 (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

-dgs real 0
 default value for solvation free energy per area (kJ/mol/nm2)



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