-a no automatic cartesian -> zmat conversion
-b use orbitals of first point on opt. runs
-c0.5 change depth of shading
-d print debug information
-e DMAREL INPUT: Use est set of parameters
-f PDB: build connectivity from cartesian coordinates
-g PDB: always calculate Helix/Sheet information
-geom XXXxYYY-xxx-yyy
XXX and YYY are the size of the window
xxx and yyy are the position of the window
-h print commandline flags
-hoff switch of hydrogen bonds
-hdmin x mininum hydrogen bond distance (Ang)
-hdmax x maximum hydrogen bond distance (Ang)
-hamin x mininum hydrogen bond angle (Degrees)
-hamax x maximum hydrogen bond angle (Degrees)
-i opt fdat files:
opt=1 standardise H-C, H-N
opt=2 1 + standardise phenyl rings
-j num maximum number of gifs to write
-k num select color of labels (0-15)
(gmolden only).
-l dont display molden logo
-oppp change default plotfilename from 'plot' to 'ppp'
-n dont add hydrogens to PDB fil
-m turn off the beep sounds
-p2.0 change default perspective value from 0.3 to 2.0
-r fname read file with per line;
atom color(1-15) VandeWaalsRadius, (- = skip)
-s4.0 scale amplitude in normal vibrations
-u With GAMESS-US optimisation output, molden
generates a z-matrix, instead of reading from output
-v print verbose information
-w opt write all points of a movie to a file:
opt specifies format; xyz(=1) zmat(=2,mopac) VRML2.0(=3)
-x file read in file with spherical atomic densities
-y 1.0 threshold for printing displacement vectors
of normal modes to postscript file
-z create high quality opengl coils
-A Keep order of atoms when creating a Z-matrix
-C Color postscript (default=mono, except for PDB)
-D opt DMA mode:
0 = atomic sites only (default)
1 = atomic+halfway-bond sites
2 = no shift of overlap dens. of conn. atoms
-E DMAREL input: use coordinates from multipoles
-G 0.6 Grid width colour coded ESP potential map
-H GAMESS-US: do normal modes when HSSEND=.TRUE.
-I dont use shaders, if available
-L display both neg. and pos. contour in space
plot of the laplacian
-1 use only the lower half of the cubic grid
used for the space type plot
-2 use only the upper half of the cubic grid
used for the space type plot
-M MonoChrome postscript
-N Check for mpi, to run ambfor/ambmd in parallel
-O switch off multiple structures handling
-P PDB: treat all input files as PDB files
-Q support for older StarNet xwin32 (ver. 6)
-R npts adjust the gridsize in points
-S start with shade off
-T treat all input files as TINKER xyz files
-U do not use opengl shaders
-V fname VRML density filename
-W Write VRML2.0 instead of VRML1.0
-X When reading XMOL cartesian format
-Z Map the Z-matrix file mapfile onto crystal
mapfile contains Z-matrix followed by keyword
MAP and per line an integer that maps a
Z-matrix line onto a cartesian line
-= Use gamess-us dialect of gaussian zmat writing