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)

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)