g_sas


Main Table of Contents

VERSION 3.0
Tue 24 Jul 2001


Description

g_sas computes hydrophobic 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 area can be plotted per atom and per residue as well (option -ao). In combination with the latter option an itp file can be generated (option -i) which can be used to restrain surface atoms.

Files

optionfilenametypedescription
-f traj.xtc Input Generic trajectory: xtc trr trj gro g96 pdb
-s topol.tpr Input Generic run input: tpr tpb tpa
-o area.xvg Output xvgr/xmgr file
-r resarea.xvg Output xvgr/xmgr file
-q connelly.pdb Output, Opt. Protein data bank file
-ao atomarea.xvg Output, Opt. xvgr/xmgr file
-n index.ndx Input, Opt. Index file
-i surfat.itp Output, Opt. Include file for topology

Other options

optiontypedefaultdescription
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line options
-nice int 19 Set the nicelevel
-b time -1 First frame (ps) to read from trajectory
-e time -1 Last frame (ps) to read from trajectory
-dt time -1 Only use frame when t MOD dt = first time (ps)
-[no]w bool no View output xvg, xpm, eps and pdb files
-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
-minarea real 0.5 The maximum charge (e, absolute value) of a hydrophobic atom
-skip int 1 Do only every nth frame
-[no]prot bool yes Output the protein to the connelly pdb file too


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