The file is located at: data/colour_table.data
The first line in the colour file is a comment. The following colour table (a small part of it in fact) contains the rgb code and the name defined for that rgb code. You can add your own colour to the table by editing the file. The colour table file is also used by the colour browsers. As it is now implemented only the first 200 colours are included in the browser.
The rgb codes and their names:
* Colour table to be used by gOpenMol (1997-11-21) 255 255 255 white 0 0 0 black 255 0 0 red 0 255 0 green 0 0 255 blue 255 0 255 magenta 255 255 0 yellow 192 192 192 gray 238 130 238 violet 165 42 42 brown 0 255 255 cyan 255 192 48 bright mustard 134 26 26 dark firebrick 255 128 144 miami pink 80 255 255 miami turquoise 80 40 30 dark brown 128 0 0 dark red 255 250 250 snow 248 248 255 ghost white 245 245 245 white smoke 255 239 213 papaya whip 255 218 185 peach puff 255 228 181 moccasin 255 248 220 cornsilk 255 255 240 ivory 255 250 205 lemon chiffon 245 255 250 mint cream 240 255 255 azure 240 248 255 alice blue 230 230 250 lavender 255 240 245 lavender blush 105 105 105 dim gray 112 128 144 slate gray 211 211 211 light grey 25 25 112 midnight blue 0 0 128 navy blue 175 238 238 pale turquoise 0 206 209 dark turquoise 0 100 0 dark green 220 220 220 gainsboro 253 245 230 old lace 250 240 230 linen 255 235 205 blanched almond 255 228 196 bisque 255 245 238 seashell 240 255 240 honeydew 105 105 105 dim grey . . .
The gOpenMol GUI uses sliders for dynamic colour selection but colour names can be used in the line command mode.
The following data is taken from APPENDIX B of the QUANTA Reference Manual 1990.
The titles of the columns in the atom_param.data file are:
(1): Atom type number (type). (2): Bonding radius (bndrad). (3): van der Waals spheres radius (vdwrad). (4): Sphere radius (plurad) in plots. (Not used in gOpenMol). (5): Value (global) is used in global search for bonds. (6,7): Value (emin and rmin) used in the calculation of van der Waals and electrostatic energy. (8): Atom polarizabilities (patom). (9): The atom is either a hydrogen bond acceptor (A), donor (D or E), or not hydrogen bonded (N) (10): The CHARMm atom type (atype). (11): Atom mass (mass).
Example:
(1) (2) (3) (4) (5) (6) (7) (8) (9) (10) (11) Type bndrad vdwrad plurad global emin rmin patom hbond atype mass 1 0.40 0.95 0.100 F -0.0498 0.8 0.044 D H 1.008
The parameters in QUANTA 3.0 are similar to those used in Version 21 of CHARMm. The emin rmin values differ for HA and all metals; bndrad differs for hydrogens. Atoms with Mxx are metals; atoms with Xxx are halogens.
If you wish to extend the parameter file to include your own atom types, it is recommended to use atom numbers greater than 300.
The format of the atom.dic file is as following.
The first position (1) is the residue name, the next position (2)
is the atom name, third position (3) is the atom type according
to the CHARMm type and as the last position (4) comes the atom charge.
The residue and atom names are restricted to 4 characters, atomic
type is an integer and the charge is a floating point number.
The user can also use the symbols '*' and '?' for or in the
residue and atom names where '*' matches any characters to the end
and '?' matches any character at that particular point.
Your own molecules can be added to the end of the file
before the default atom types.
Example of an atom dictionary file:
The user can easily add his/her favourite molecules to
the end of this file before the default atom types.
There are two files supplied atom.dic atom types
for amino acids with polar hydrogens and atomh.dic
for amino acids with all hydrogen atoms. The files can
be found in directory .../data. These files are made from
files of the QUANTA package by MSI.
Input lines:
Example:
If the input is made by gOpenMol the file looks like the following:
The main difference is now that the atom names and coordinates
are included in the input file.
The program can be run with the command
density < density.inp > density.out.
The program has the following options:
-ofile.name
Write the orbital or density mesh into file file.name instead of
the default file orbital.plt.
Appendix III
The format of the atomXXX.dic files
*Amino acid dictionary, polar hydrogens only, CHARMm20.3 parameters (From QUANTA)
GLY CA 12 0.100
PRO N 33 -0.200
* N 32 -0.350
* NT 36 -0.100
* H 1 0.250
* HT?? 2 0.350
* CA 11 0.100
* C 14 0.550
* O 40 -0.550
* OT 44 -0.550
* CT1 10
* CT2 10
ALA CB 13 0.000
ARG CB 12 0.000
ARG CG 12 0.000
ARG CD 12 0.100
ARG NE 32 -0.400
ARG HE 1 0.300
ARG CZ 14 0.500
ARG NH? 37 -0.450
ARG HH?? 2 0.350
ASN CB 12 0.000
ASN CG 14 0.550
ASN OD? 40 -0.550
ASN ND? 32 -0.600
ASN HD?? 1 0.300
ASP CB 12 -0.160
ASP CG 14 0.360
ASP OD? 43 -0.600
ASP HD? 2 1.000
CYS CB 12 0.019
CYS SG 70 -0.019
CYS HG 1 0.000
GLN CB 12 0.000
GLN CG 12 0.000
GLN CD 14 0.550
GLN OE? 40 -0.550
GLN NE? 32 -0.600
GLN HE?? 1 0.300
GLU CB 12 0.000
GLU CG 12 -0.160
GLU CD 14 0.360
GLU OE? 43 -0.600
GLU HE? 2 1.000
HIS CB 12 0.000
HIS CG 21 0.100
HIS ND? 34 -0.400
HIS HD? 1 0.300
HIS CD? 23 0.100
HIS CE? 23 0.300
HIS NE? 34 -0.400
ILE CB 11 0.000
ILE CG1 12 0.000
ILE CG2 13 0.000
ILE CD? 13 0.000
LEU CB 12 0.000
LEU CG 11 0.000
LEU CD? 13 0.000
LYS CB 12 0.000
LYS CG 12 0.000
LYS CD 12 0.000
LYS CE 12 0.250
LYS NZ 36 -0.300
LYS HZ? 2 0.350
MET CB 12 0.000
MET CG 12 0.060
MET SD 70 -0.120
MET CE 13 0.060
PHE CB 12 0.000
PHE CG 22 0.000
PHE CD? 24 0.000
PHE CE? 24 0.000
PHE CZ 24 0.000
PRO CB 12 0.000
PRO CG 12 0.000
PRO CD 12 0.100
SER CB 12 0.250
SER OG 45 -0.650
SER HG 1 0.400
THR CB 11 0.250
THR OG? 45 -0.650
THR HG? 1 0.400
THR CG? 13 0.000
TRP CB 12 0.000
TRP CG 21 -0.030
TRP CD1 23 0.060
TRP CD2 26 0.100
TRP NE1 34 -0.360
TRP HE1 1 0.300
TRP CE2 26 -0.040
TRP CE3 24 -0.030
TRP CZ? 24 0.000
TRP CH? 24 0.000
TYR CB 12 0.000
TYR CG 22 0.000
TYR CD? 24 0.000
TYR CE? 24 0.000
TYR CZ 22 0.250
TYR OH 45 -0.650
TYR HH 1 0.400
VAL CB 11 0.000
VAL CG? 13 0.000
WAT O??? 47 -0.834
WAT H??? 4 0.417
H2O O??? 47 -0.834
H2O H??? 4 0.417
SOL O??? 47 -0.834
SOL H??? 4 0.417
HOH O??? 47 -0.834
HOH H??? 4 0.417
DOD O??? 47 -0.834
DOD D??? 4 0.417
TIP O??? 47 -0.834
TIP H??? 4 0.417
TIP3 OH2 47 -0.834
TIP3 H1 4 0.417
TIP3 H2 4 0.417
NAP NA1 81 1.000
#
# New molecule definitions come here
#
** N??? 32
** C??? 10
** S??? 70
** HT?? 1
** H??? 3
** O??? 45
** P??? 60
** MFE? 86
** ZN?? 87
** MCA? 84
** ???? 499
Appendix IV
The input format to the orbital and electron density
program DENSITY. The program accepts now only wave
functions from the ICON8 program. The default name
for the wave function file is fort.7.
1) Two Title lines.
2) Name of the input file to the ICON8 program.
This file contains the atom coordinates. The coordinates
and the atom names can also be directly included here.
3) This line defines the size of the box by defining
the x-min, x-max, y-min, y-max, z-min and z-max.
4) This line defines the number of points in the x, y and z directions.
5) The first number defines t he orbital number to be calculated
and the second number gives the type: 0 = orbital plot, 1 = orbital
density and 2 = total elctron density. If the total electron
density is defined the first number (the orbital number) has no meaning.
****** test input *******
****** test input *******
@icon8.inp
fort.7
-8.3200 6.5625 -13.9597 6.2823 -2.7837 2.0980
50 50 50
41 0
Default title for: DENSITY
Default title for: DENSITY
6
0.000000 0.670000 0.000000 C
0.000000 -0.670000 0.000000 C
0.926650 1.205000 0.000000 H
-0.926650 1.205000 0.000000 H
0.926650 -1.205000 0.000000 H
-0.926650 -1.205000 0.000000 H
fort.7
-3.0 3.0 -3.0 3.0 -3.0 3.0
30 30 30
6 0