g_sas_d

Langue: en

Autres versions - même langue

Version: 250961 (debian - 07/07/09)

Section: 1 (Commandes utilisateur)

NAME

g_sas - computes solvent accessible surface area

SYNOPSIS

g_sas -f traj.xtc -s topol.tpr -o area.xvg -or resarea.xvg -oa atomarea.xvg -q connelly.pdb -n index.ndx -i surfat.itp -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -solsize real -ndots int -qmax real -[no]f_index -minarea real -[no]pbc -[no]prot -dgs real

DESCRIPTION

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 -pbc option.

FILES

-f traj.xtc Input
 Generic trajectory: xtc trr trj gro g96 pdb 

-s topol.tpr Input
 Generic run input: tpr tpb tpa xml 

-o area.xvg Output
 xvgr/xmgr file 

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

-oa atomarea.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 

OTHER OPTIONS

-[no]h no
 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)

-[no]w no
 View output xvg, xpm, eps and pdb files

-[no]xvgr yes
 Add specific codes (legends etc.) in the output xvg files for the xmgrace program

-solsize 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

-[no]f_index no
 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)

-[no]pbc yes
 Take periodicity into account

-[no]prot yes
 Output the protein to the connelly pdb file too

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

SEE ALSO

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.