7.1. xtp_map¶
7.1.1. help¶
7.1.1.1. NAME¶
xtp_map - Part of the VOTCA package
7.1.1.2. SYNOPSIS¶
xtp_map [OPTIONS]
xtp_map [–help]
7.1.1.3. DESCRIPTION¶
Generates QM|MD topology
7.1.1.4. OPTIONS¶
Allowed options:
-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
-t [ --topology ] arg topology
-c [ --coordinates ] arg coordinates or trajectory
-s [ --segments ] arg definition of segments and fragments
-m [ --makesegments ] write out a skeleton segments file
-f [ --file ] arg state file
-i [ --first-frame ] arg (=0) start from this frame
-b [ --begin ] arg (=0) start time in simulation
-n [ --nframes ] arg (=1) number of frames to process
--guess-bonds guess real bond connectivity from atom
positions alone (a simple,
van-der-Waals-radii-based heuristic, matching
the one VMD itself uses for visualization --
restricted to atom pairs within the same real
MD molecule only) -- ONLY if the loaded
topology genuinely has no real bond
connectivity of its own at all; never used if
real bonds are already present. Writes a real,
direct, inspectable report of every guessed
bond to guessed_bonds_report.txt -- always
review this before trusting the guessed
connectivity for anything at all, since this
heuristic can be genuinely wrong (see VMD's
own developers' documented caveats about it).