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xplor2gmx(1) [debian man page]

xplor2gmx(1)						      General Commands Manual						      xplor2gmx(1)

NAME
xplor2gmx - Convert XPLOR distance restraints to Gromacs format SYNOPSIS
xplor2gmx (residue offset) input.pdb DESCRIPTION
xplor2gmx reads an XPLOR input file with distance restraint data as sometimes is found in the pdb database (http://www.pdb.org). From this input file dihedral restrints should be removed, such that only distance restraints are left. The script can handle ambiguous restraints. It converts the distance restraints to GROMACS format. A restraints file (.dat) should be provided on STDIN, and a suitable output file (.itp) is sent to STDOUT. EXAMPLES
xplor2gmx.pl 33 conf.pdb < restraints.dat > disre.itp OPTIONS
xplor2gmx requires two command line options: first, the residue offset (integer); second, the .pdb filename. The pdb file must have cor- rect atom numbers. SEE ALSO
gromacs(7) GROMACS suite, Version 4.0 13 Oct 2008 xplor2gmx(1)

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g_anadock(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				      g_anadock(1)

NAME
g_anadock - cluster structures from Autodock runs VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_anadock -f eiwit.pdb -ox cluster.pdb -od edocked.xvg -of efree.xvg -g anadock.log -[no]h -[no]version -nice int -xvg enum -[no]free -[no]rms -cutoff real DESCRIPTION
g_anadock analyses the results of an Autodock run and clusters the structures together, based on distance or RMSD. The docked energy and free energy estimates are analysed, and for each cluster the energy statistics are printed. An alternative approach to this is to cluster the structures first using g_cluster and then sort the clusters on either lowest energy or average energy. FILES
-f eiwit.pdb Input Protein data bank file -ox cluster.pdb Output Protein data bank file -od edocked.xvg Output xvgr/xmgr file -of efree.xvg Output xvgr/xmgr file -g anadock.log Output Log file OTHER OPTIONS
-[no]hno Print help info and quit -[no]versionno Print version info and quit -nice int 0 Set the nicelevel -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -[no]freeno Use Free energy estimate from autodock for sorting the classes -[no]rmsyes Cluster on RMS or distance -cutoff real 0.2 Maximum RMSD/distance for belonging to the same cluster SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_anadock(1)
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