Usage: direx [option1] [option2] ...

Input options

-f <all.par> Read run parameters
-pdb <conf.pdb> Read topology and coordinates from PDB file
-s <topol.tpr> Read topology from Gromacs run input file
-p <init.pdb> Reads PDB coordinates. The [-psf] option needs this. If used together with [-s], the coordinates in <topol.tpr> are ignored. If used together with [-pdb], <init.pdb> is used as the starting structure.
-psf <topol.psf> Read X-plor topology. Needs [-p] option
-d <file> Reads CONCOORD distance restraints
-refden <refden.pdb> Reference structure for the DEN
-iden <den.dat> Read DEN restraints
-expd <expd.dat> Reads additional harmonic distance restraints
-map <map.[xplor/mrc]> Reads electron density map in ASCII-XPLOR format if "self", a map will be created. In that case you can use the option -map_apix
-map_apix <apix> Sets map grid spacing in Angstrom. Only used if -map self to set the grid spacing in Angstrom.
-secstr <secstr.dat> Reads secondary structure information.
-ncs <ncs.dat> Reads NCS (non-crystallographic symmetry) restraints which is e.g. used to keep identical subunits similar.
-posre <posre.dat> Reads positions restraints.

Output options

-ox <traj.xtc> Write file in Gromacs-compatible xtc format
-op <out.pdb> Write structures as single PDB files. A number will be added to the filename
-oe <energy.dat> Write electrostatic energy
-oden <den.dat> Write DEN restraints
-otop <top.dat> Write detected topology
-cur <current.pdb> Write out current structure during the simulation
-curmap <name.[xplor/mrc]> Write current model density
-curdifmap <name.[xplor/mrc]> Write current model difference density
-oinmap <name.[mrc/xplor]> Write input density map
-mapcc <mapcc.dat> Write map correlation

More options
-seed <value> Seed for random number generator
-v Be verbose
-h Show these details