g_sas_d (1) - Linux Manuals
g_sas_d: computes solvent accessible surface area
NAMEg_sas - computes solvent accessible surface area
SYNOPSISg_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
DESCRIPTIONg_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.
FILES-f traj.xtc Input
-nice int 19
-b time 0
-e time 0
-dt time 0
-probe real 0.14
-ndots int 24
-qmax real 0.2
-minarea real 0.5
-dgs real 0