do_dssp(1) [debian man page]
do_dssp(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c do_dssp(1) NAME
do_dssp - assigns secondary structure and calculates solvent accessible surface area VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
do_dssp -f traj.xtc -s topol.tpr -n index.ndx -ssdump ssdump.dat -map ss.map -o ss.xpm -sc scount.xvg -a area.xpm -ta totarea.xvg -aa aver- area.xvg -[no]h -[no]version -nice int -b time -e time -dt time -tu enum -[no]w -xvg enum -sss string DESCRIPTION
do_dssp reads a trajectory file and computes the secondary structure for each time frame calling the dssp program. If you do not have the dssp program, get it from http://swift.cmbi.ru.nl/gv/dssp. do_dssp assumes that the dssp executable is located in /usr/local/bin/dssp. If this is not the case, then you should set an environment variable DSSP pointing to the dssp executable, e.g.: setenv DSSP /opt/dssp/bin/dssp The structure assignment for each residue and time is written to an .xpm matrix file. This file can be visualized with for instance xv and can be converted to postscript with xpm2ps. Individual chains are separated by light grey lines in the .xpm and postscript files. The number of residues with each secondary structure type and the total secondary structure ( -sss) count as a function of time are also written to file ( -sc). Solvent accessible surface (SAS) per residue can be calculated, both in absolute values (A2) and in fractions of the maximal accessible surface of a residue. The maximal accessible surface is defined as the accessible surface of a residue in a chain of glycines. Note that the program g_sas can also compute SAS and that is more efficient. Finally, this program can dump the secondary structure in a special file ssdump.dat for usage in the program g_chi. Together these two programs can be used to analyze dihedral properties as a function of secondary structure type. FILES
-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -s topol.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb -n index.ndx Input, Opt. Index file -ssdump ssdump.dat Output, Opt. Generic data file -map ss.map Input, Lib. File that maps matrix data to colors -o ss.xpm Output X PixMap compatible matrix file -sc scount.xvg Output xvgr/xmgr file -a area.xpm Output, Opt. X PixMap compatible matrix file -ta totarea.xvg Output, Opt. xvgr/xmgr file -aa averarea.xvg Output, Opt. xvgr/xmgr file OTHER OPTIONS
-[no]hno Print help info and quit -[no]versionno Print version 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) -tu enum ps Time unit: fs, ps, ns, us, ms or s -[no]wno View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -sss string HEBT Secondary structures for structure count SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 do_dssp(1)
Check Out this Related Man Page
g_sas(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_sas(1) NAME
g_sas - computes solvent accessible surface area VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
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 -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -probe 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 gener- ated 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 average and standard devia- tion of the area over the trajectory 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. For example, in ice Ih, one can easily fit water molecules in the pores which would yield a volume that is too low, and surface area and density that are both too high. FILES
-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -s topol.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb -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 OTHER OPTIONS
-[no]hno Print help info and quit -[no]versionno Print version 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]wno View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -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 -[no]f_indexno 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]pbcyes Take periodicity into account -[no]protyes 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 GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_sas(1)