xplor2gmx(1) General Commands Manual xplor2gmx(1)NAME
xplor2gmx - Convert XPLOR distance restraints to Gromacs format
xplor2gmx (residue offset) input.pdb
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.
xplor2gmx.pl 33 conf.pdb < restraints.dat > disre.itp
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)
Check Out this Related Man Page
g_anadock(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_anadock(1)NAME
g_anadock - cluster structures from Autodock runs
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
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
FILES -f eiwit.pdb Input
Protein data bank file
-ox cluster.pdb Output
Protein data bank file
-od edocked.xvg Output
-of efree.xvg Output
-g anadock.log Output
Print help info and quit
Print version info and quit
-nice int 0
Set the nicelevel
-xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none
Use Free energy estimate from autodock for sorting the classes
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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