Appendix


Appendix I

The format of the colour file

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.


Appendix II


The format of the data/atom_param.data file

This file contains data for the display of atoms and some other useful parameters as the Lennard-Jones parameters.

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.


Appendix III


The format of the atomXXX.dic files

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:

*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 

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.


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.

Input lines:

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. 

Example:

****** 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

If the input is made by gOpenMol the file looks like the following:

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

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 V


The probe surface program PROBESURF generates a mesh with grid values from 0 to 100. The value 100 is at the vdW value and value 0 is at the vdW + max. probe diameter value.

It is possible to generate the surface for different probe values. The method is based on the article by R. Voorintholt et al. (Voorintholt R., Koster M.T. , Vegter G. , Vriend G. and Hol W.G.J., "A very fast program for visualizing protein surfaces, channels and cavities", J. Mol. Graphics 7 (1989) 243-245)

The input format to the probe surface program PROBESURF.

Input lines:

1) Two Title lines.

2) Number of atoms.

3) All this on one line:
     1: Running atom number.
     2: Segment name.
     3: Residue name.
     4: Atom name.
     5: X coordinate.
     6: Y coordinate.
     7: Z coordinate.
     8: van Der Waals radius. 

4) This line defines the size of the box by defining the x-min, 
   x-max, y-min, y-max, z-min and z-max.

5) This line defines the number of points in the x, y and z directions. 

6) The maximum probe radius.

Example:

Default title for: PROBESURF
Default title for: PROBESURF
27 
1 OXAZ OXAZ C1 0.745450 1.329030 -0.112310 1.770000 
2 OXAZ OXAZ C2 -0.649260 1.283460 -0.047400 1.770000 
3 OXAZ OXAZ C3 -1.305230 0.051170 0.008740 1.770000 
4 OXAZ OXAZ C4 -0.569310 -1.138250 0.000150 1.770000 
5 OXAZ OXAZ C5 0.826120 -1.089110 -0.064870 1.770000 
6 OXAZ OXAZ C6 1.483480 0.142830 -0.121060 1.770000 
7 OXAZ OXAZ C7 -1.240880 -2.420370 0.058060 1.770000 
8 OXAZ OXAZ C8 -1.934730 -4.549460 0.134900 1.770000 
9 OXAZ OXAZ C9 -3.122750 -3.648180 0.170320 1.770000 
10 OXAZ OXAZ O10 -2.574450 -2.443880 0.119710 1.520000 
11 OXAZ OXAZ N11 -0.784090 -3.681460 0.063780 1.600000 
12 OXAZ OXAZ O12 -4.320040 -3.925030 0.231080 1.520000 
13 OXAZ OXAZ C13 -2.043830 -5.884680 0.168140 1.770000 
14 OXAZ OXAZ C14 -1.244540 -8.066310 0.177640 1.770000 
15 OXAZ OXAZ C15 0.052310 -8.899060 0.135760 1.770000 
16 OXAZ OXAZ O16 -0.918760 -6.663430 0.133020 1.520000 
17 OXAZ OXAZ H17 1.252970 2.282310 -0.155740 0.900000 
18 OXAZ OXAZ H18 -1.221770 2.200130 -0.040530 0.900000 
19 OXAZ OXAZ H19 -2.384360 0.009980 0.059090 0.900000 
20 OXAZ OXAZ H20 1.395210 -2.008100 -0.071530 0.900000 
21 OXAZ OXAZ H21 2.562540 0.178850 -0.171300 0.900000 
22 OXAZ OXAZ H22 -3.033270 -6.342320 0.223210 0.900000 
23 OXAZ OXAZ H23 -1.867540 -8.323760 -0.679230 0.900000 
24 OXAZ OXAZ H24 -1.786000 -8.286150 1.098030 0.900000 
25 OXAZ OXAZ H25 -0.196250 -9.959719 0.167400 0.900000 
26 OXAZ OXAZ H26 0.675080 -8.646710 0.994020 0.900000 
27 OXAZ OXAZ H27 0.595610 -8.681110 -0.783720 0.900000 
-15.242029 15.242029 -15.242029 15.242029 -15.242029 15.242029 
60 60 60
1.900000 

The program has the following options:

-ofile.name

Write the probe surface mesh into file file.name instead of the default file probesurf.plt.

The program probsurf is located in the bin/ directory.

When you display a probsurf generated *.plt grid file using the isocontour display engine remember that the display value range is between 100. and 0.0

Example of a probesurface: The water surface around the cellobiohydrolase I (CBH I) tail.


Appendix VI


The VSS program calculates the electrostatic potential created by the electronic distribution and the nuclei of a molecule in the surrounding space. The electronic distribution is supposed to be obtained from the ICON8 program. It correaponds to approximation II of "Molecular electrostatic potentials: comparison of ab initio and CNDO results" by C. Giessner-Prettre and A. Pullman, Theoret. Chim. Acta (Berl.) (1972) 25, 83-88. This program is a direct translation of the fortran version into c.

The input is as follows :

(1) Title. 
(2) Title. 
(3) Title. 
(4) NAT = number of atoms 
    NH = number of hydrogens 

    IU = 0 or 1. 

    IU = 0 the coordinates are given in atomic units 

    IU = 1 the coordinates are given in angstrom units 

(5) the following NAT cards 

    X, Y and Z coordinates for atom i 

    IZ = number of valence electrons 

    (The hydrogen atoms must be entered last).


(6) the following NAT cards 

    gross atomic population and screening constant for atom i 

(7) Integer always 2 (not used) 

(8) Xmin, Xmax, Ymin, Ymax, Zmin and Zmax values to define the box. 

(9) Number of points in the X-, Y- and Z-directions.

Example:

*******NO_INFO******* 
*******NO_INFO******* 
ETHYLENE 
6 4 1 
0.0000 0.6700 0.0000 4 
0.0000 -0.6700 0.0000 4 
0.9267 1.2050 0.0000 1 
-0.9267 1.2050 0.0000 1 
0.9267 -1.2050 0.0000 1 
-0.9267 -1.2050 0.0000 1 
4.1027 1.6250 
4.1027 1.6250 
0.9486 1.3000 
0.9486 1.3000 
0.9486 1.3000 
0.9486 1.3000 
2 
-0.9267 0.9267 -1.2050 1.2050 0.0000 0.0000 
40 40 40

The program has the following options:

-ofile.name

Write the isoenergy mesh into file file.name instead of the default file vsscont.plt.


Currently all programs except the ICON8 program are written in c. Dynamic memory allocation has been used in all the c programs. ICON8 currently accepts systems up to 1000 atoms, but can easily be modified to accept more atoms. The problem with the ICON8 code is the memory. To calculate system up to 1000 atoms needs some 150 Mbytes of memory. The other programs used dynamic memory allocation and uses very little memory.