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g_sas
Langue: en
Version: 252992 (debian - 07/07/09)
Section: 1 (Commandes utilisateur)
NAME
g_sas - computes solvent accessible surface areaSYNOPSIS
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 realDESCRIPTION
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 InputGeneric 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 noPrint 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/>.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre