| -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. |
| -turbo | Turbo mode: less accurate but much faster. |
| -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 |
