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Appendix K. Figures
K.1. Example of a PDB file
The first part of a typical PDB input file. See text. The Password 'New York, NY' is in the HEADER. See text. It is particularly important that each item of data appears in exactly the correct column or columns.
HEADER New York, NY FIRST TEST COMPND LYSOZYME SOURCE HUMAN REMARK STRUCTURE FACTORS FOR THIS COMPOUND ARE AVAILABLE ATOM 1 CA LYS 1 1.933 20.601 21.051 1.00 0.00 ATOM 2 N LYS 1 1.395 19.741 22.120 1.00 0.00 ATOM 3 C LYS 1 3.187 19.951 20.453 1.00 0.00 ATOM 4 O LYS 1 3.944 19.265 21.154 1.00 0.00 ATOM 5 CB LYS 1 2.378 21.823 21.855 1.00 0.00 ATOM 6 CG LYS 1 3.351 22.720 21.132 1.00 0.00 ATOM 7 CD LYS 1 3.711 23.932 21.970 1.00 0.00 ATOM 8 CE LYS 1 4.513 24.958 21.185 1.00 0.00 ATOM 9 NZ LYS 1 4.654 26.233 21.897 1.00 0.00 ATOM 10 CA VAL 2 4.638 19.766 18.500 1.00 0.00 ATOM 11 N VAL 2 3.386 20.166 19.169 1.00 0.00 ATOM 12 C VAL 2 5.414 21.073 18.300 1.00 0.00 ATOM 13 O VAL 2 5.028 21.972 17.536 1.00 0.00 ATOM 14 CB VAL 2 4.374 19.081 17.166 1.00 0.00 ATOM 15 CG1 VAL 2 5.660 18.596 16.491 1.00 0.00 ATOM 16 CG2 VAL 2 3.468 17.856 17.298 1.00 0.00 ATOM 17 CA PHE 3 7.389 22.369 18.879 0.00 0.00 ATOM 18 N PHE 3 6.530 21.204 19.039 0.00 0.00 ATOM 19 C PHE 3 8.111 22.337 17.546 0.00 0.00 ATOM 20 O PHE 3 8.510 21.276 17.017 0.00 0.00 ATOM 21 CB PHE 3 8.508 22.351 19.907 0.00 0.00 ATOM 22 CG PHE 3 8.057 22.866 21.254 0.00 0.00 ATOM 23 CD1 PHE 3 8.316 24.154 21.630 0.00 0.00 ATOM 24 CE1 PHE 3 7.884 24.616 22.900 0.00 0.00 ATOM 25 CZ PHE 3 7.176 23.840 23.762 0.00 0.00 ATOM 26 CE2 PHE 3 6.854 22.577 23.355 0.00 0.00 ATOM 27 CD2 PHE 3 7.302 22.052 22.088 0.00 0.00 ATOM 28 CA GLU 4 9.393 23.654 16.018 1.00 0.00 ATOM 29 N GLU 4 8.378 23.548 17.076 1.00 0.00 ATOM 30 C GLU 4 10.777 23.661 16.641 1.00 0.00 ATOM 31 O GLU 4 10.892 24.090 17.810 1.00 0.00 ATOM 32 CB GLU 4 9.244 24.965 15.198 1.00 0.00 ATOM 33 CG GLU 4 7.883 25.199 14.598 1.00 0.00 ATOM 34 CD GLU 4 8.004 25.994 13.310 1.00 0.00 ATOM 35 OE2 GLU 4 8.299 25.389 12.211 1.00 0.00 ATOM 36 OE1 GLU 4 7.815 27.267 13.332 1.00 0.00 |
K.2. Relationship between Programmes, Directives, Files and Channels
Channel INPB is provided in order to accept a second GRIDKONT output from another GRID run, so that a difference map GRABKOND can be computed by Programme GRAB. See text.
K.3. The lineprinter output file GRINLOUT
Input directives are first printed for checking purposes, and then a list of messages about input from the Protein Data Bank file. In this example the COMPND, SOURCE and REMARK lines are just copied as information, but have no influence on the output file GRINKOUT. The HEADER is copied to GRINLOUT as a record, and will also appear in GRINKOUT. It still includes the Password 'New York, NY'.
In the present case the PDB file did not finish with an OXT atom at the carboxy terminal, but the last oxygen was called OE by mistake. Error message N620 was therefore generated. Moreover, a line of undecipherable characters also occured in the PDB file, and this was copied to GRINLOUT for information! It must be removed by editing PDB. Finally, the GRINLOUT file ends with a general message summarising the overall quality of the PDB input file.
DIRECTIVES
==========
CODE VALUE
IDIR 5
INAT 10
INKO 11
LOUT 6
KOUT 20
ALHY 0.0400
EFHH 1.0000
IHVA 0
LEVL 1
MOVE 1
QQHY 0.0000
VDHY 0.6000
MESSAGES CONCERNING INPUT FROM THE BROOKHAVEN DATA BANK:-
HEADER New York, NY FIRST TEST
COMPND LYSOZYME
SOURCE HUMAN
REMARK STRUCTURE FACTORS FOR THIS COMPOUND ARE AVAILABLE
(N620-E) THIS MOLECULE CONTAINS AN EXTRA ATOM:
ATOM 1029 OE VAL 130 22.905 30.723 20.555 0.00 0.00
[$:;"{}=\/[[3[]2 4${@}{++)865]{4 *"";/:?"{}+09[]';(*5$ @]
*** THANK YOU FOR USING PROGRAM GRIN ***
....BUT IT IS IMPORTANT TO CHECK YOUR PDB INPUT FILE....
................................................
AS IT MAY CONTAIN UNACCEPTABLE ERRORS
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K.4. The first part of an input file GRUB
The column of XLETAS should line up vertically as shown, and a displaced XLETA may indicate that there is something wrong with a record. Notes are printed to the right of the column of XLETAS, but they cannot be FULLY displayed in this figure because a format with 132 columns is needed.
Attention is drawn to the tabulated values 00 00 for ID and IA. These are "dummy" values for the number of hydrogen bonds, and the actual numbers are defined by the TYPE which is the number in the next column. You can edit datafile GRUB and replace either or both of these 00 values with positive integers in order to overwrite the numbers defined by the TYPE.
The Hydrogen Charge columns are not used, unless explicit ATOM records for hydrogens are supplied in the PDB file.
************************ X
* * X
* DATAFILE GRUB * X
* * X
* Version 20 * X
************************ X
X NOTE:
MOLE!----------------!------!--------------------!--------X The "
CULE! VAN DER WAALS !CHARGE! HYDROGEN BOND ! HYDRO- X (1)
OR ! PARAMETERS ! ! PARAMETERS ! GEN X
ATOM! VDWR NEFF ALPH ! Q !EMIN RMIN ID IA TYPE! CHARGE X (2)
NAME!----------------!------!--------------------!--------X When
! ! ! ! X then
! ! ! ! X calcu
! ! X
A 24 X ADEN
P 1.90 10. 3.00 -0.050 0.00 0.00 00 00 00 0.000 0 X NOTE:
O1P 1.60 6. 2.14 -0.650 -1.50 1.50 00 00 64 0.000 0 X
O2P 1.60 6. 2.14 -0.650 -1.50 1.50 00 00 64 0.000 0 X
O3P 1.60 6. 2.14 -0.650 -1.50 1.50 00 00 64 0.000 0 X NOTE:
: : : : : : : : : : : :
: : : : : : : : : : : :
: : : : : : : : : : : :
N1 1.60 6. 1.10 -0.120 -4.00 1.55 00 00 97 0.000 0 X
C2 1.90 6. 2.07 0.150 0.00 0.00 00 00 25 0.005 1 X
N3 1.60 6. 1.10 -0.120 -4.00 1.55 00 00 97 0.000 0 X
C4 1.85 5. 1.65 0.050 0.00 0.00 00 00 25 0.000 0 X
ABU 7 X AMINO
N 1.65 7. 1.40 -0.080 -4.00 1.60 00 00 -1 0.070 1 X
CA 1.85 6. 1.35 0.075 0.00 0.00 00 00 00 0.020 1 X
C 1.80 5. 1.65 0.350 0.00 0.00 00 00 00 0.000 0 X
O 1.60 6. 0.84 -0.365 -4.50 1.40 00 00 8 0.000 0 X
CB 1.90 7. 1.77 0.023 0.00 0.00 00 00 00 0.020 2 X
CG 1.95 8. 2.17 -0.003 0.00 0.00 00 00 00 0.010 3 X
OXT 1.60 6. 2.14 -0.560 -4.50 1.40 00 00 8 0.000 0 X
ACE 4 X ACETY
CH3 1.95 8. 2.17 0.010 0.00 0.00 00 00 00 0.010 3 X NOTE:
C 1.80 5. 1.65 0.345 0.00 0.00 00 00 00 0.000 0 X
O 1.60 6. 0.84 -0.355 -4.50 1.40 00 00 8 0.000 0 X |
K.5. The first part of a GRINKOUT file
The first part of a GRINKOUT file intended as input for the next Programme GRID. See text. Note that Programme GRIN has used the first column in order to renumber each line with a consistent incrementing series of line numbers.
Directive MOVE=1 when GRIN prepared this file, and column 5 therefore has the numbers 1 and 0 showing Target atoms in the Core (1) and in flexible parts (0) of the Target. The last column is the Van der Waals (VDWR) radius copied from Datafile GRUB, and the two columns before it define the permitted movement of flexible atoms. These two columns only contain data when there is a zero in column 5. The Password 'New York,NY' is still part of the HEADER.
132-Column format is needed to display this file fully, and each line in this figure has therefore been curtailed. The Energy Variables after VDWR cannot be seen. They are off-page to the right.
New York, NY FIRST TEST
1 2 N LYS 1 1.395 19.741 22.120 0.00 0.00 1.75
2 1 CA LYS 1 1.933 20.601 21.051 0.00 0.00 1.85
3 3 C LYS 1 3.187 19.951 20.453 0.00 0.00 1.80
4 4 O LYS 1 3.944 19.265 21.154 0.00 0.00 1.60
5 5 CB LYS 1 2.378 21.823 21.855 0.00 0.00 1.90
6 6 CG LYS 0 3.351 22.720 21.132 1.60 0.27 1.90
7 7 CD LYS 0 3.711 23.932 21.970 1.60 0.27 1.90
8 8 CE LYS 1 4.513 24.958 21.185 0.00 0.00 1.90
9 9 NZ LYS 0 4.654 26.233 21.897 1.60 0.27 1.75
10 11 N VAL 1 3.386 20.166 19.169 0.00 0.00 1.65
11 10 CA VAL 1 4.638 19.766 18.500 0.00 0.00 1.85
12 12 C VAL 1 5.414 21.073 18.300 0.00 0.00 1.80
13 13 O VAL 1 5.028 21.972 17.536 0.00 0.00 1.60
14 14 CB VAL 1 4.374 19.081 17.166 0.00 0.00 1.85
15 15 CG1 VAL 0 5.660 18.596 16.491 1.73 1.53 1.95
16 16 CG2 VAL 0 3.468 17.856 17.298 1.73 1.53 1.95
17 18 N PHE 1 6.530 21.204 19.039 0.00 0.00 1.65
18 17 CA PHE 1 7.389 22.369 18.879 0.00 0.00 1.85
19 19 C PHE 1 8.111 22.337 17.546 0.00 0.00 1.80
20 20 O PHE 1 8.510 21.276 17.017 0.00 0.00 1.60
21 21 CB PHE 1 8.508 22.351 19.907 0.00 0.00 1.90
22 22 CG PHE 1 8.057 22.866 21.254 0.00 0.00 1.85
23 23 CD1 PHE 1 8.316 24.154 21.630 0.00 0.00 1.90
24 27 CD2 PHE 1 7.302 22.052 22.088 0.00 0.00 1.90
25 24 CE1 PHE 1 7.884 24.616 22.900 0.00 0.00 1.90
26 26 CE2 PHE 1 6.854 22.577 23.355 0.00 0.00 1.90
27 25 CZ PHE 0 7.176 23.840 23.762 1.60 0.27 1.90 |
K.6. Sample of directives and parameters for Grid
These input instructions were prepared by hand. The second method was used in this case, for inputting the directives LONT INPT and KONT. This file of directives would be suitable for Unix. Note that LONT comes first in the list.
The directives allocate the input channels for GRIDLONT, GRINKOUT and GRIDKONT. Note that the channel number for "grinkout.dat" has been changed to 9, and that the file names are in small letters for Unix. The directives also alter the cutoff distance FARH for hydrogen bonds; they set KWIK which speeds up the computation; and they control the printout to the lineprinter GRIDLONT with directives LENG, LEVL and NUMB. The Probe (OH2) is defined and the directive list must always finish with IEND as shown.
The parameters start with the job title: "New test with water (OH2) Probe". They then define NZ1 and NZ2 to call for five z-planes (4 5 6 7 and 8). It is not necessary to specify the explicit properties of the Probe (ie its Van der Waals radius, etc), since these are already defined by the Probe Symbol OH2.
This second method of preparing directives is particularly recommended for Unix-style operating systems. The file is called grid.in and the file names are in small letters (i.e: grinkout.dat). This file would be submitted with the instruction:
grid < grid.in
A UNIX-STYLE FILE OF DIRECTIVES FOR PROGRAMME GRID
LONT gridlont.dat
INPT 9
INPT grinkout.dat
KONT gridkont.dat
FARH 6.
KWIK 1
LENG 10
LEVL 3
NUMB 3
OH2
IEND
New test with water (OH2) Probe
4 8 |
K.7. Initial part of the GRIDLONT output
Some lines from this part of the output have been omitted.
COPYRIGHT MOLECULAR DISCOVERY LTD. ALL RIGHTS RESERVED 1999,2000 PROGRAM GRID ************************************** ************************************** DIRECTIVES ========== CODE VALUE DEEP 50.000 CLER 5.000 DPRO 4.000 NETA 0 NPLA 1 TITLE:- ===== New test with water (OH2) Probe UNITS ARE ANGSTROM, K-CAL, MOLE AND THE CHARGE ON THE ELECTRON. BOTTOM AND TOP PLANES OF GRID IN EACH DIMENSION IN ANGSTROMS:- X -7.000 36.000 Y -12.000 37.000 Z 6.000 51.000 OVERALL CHARGE ON THE TARGET AS A WHOLE: 8.000 DETAILS OF TRIAL LIGAND ATOM:- ============================ VDW RADIUS = 1.7000 NEFF = 7 POLARIZABILITY ALPHA = 1.20 ELECTRIC CHARGE = 0.000 HYDROGEN BOND GEOMETRY = TYPE 95 INTERNAL ANGLE OF PROBE = 109.5 DEGREES PROBE CAN DONATE 2 H-BONDS. PROBE CAN ACCEPT 2 H-BONDS. H-BOND ENERGY PARAMETER = -4.00 KCAL/MOLE H-BOND DISTANCE PARAMETER = 1.40 ANGSTROM |
K.8. Output table of the GRIDLONT output
The first line defines this particular GRID plane. The second and third lines were written immediately before and after the corresponding GRIDKONT array for the plane was written to file by subroutine DRITE2. As both these lines are present, the user knows that GRIDKONT has been written correctly.
This table relates to the grid point with most favourable interaction energy on this z-plane. The total energy is displayed in Kcal/mole, and the three indices NX,NY,NZ defining the position of the grid point are shown together with its real coordinates.
Each line of the table describes the interaction between the Probe (at position NX,NY,NZ) and one nearby Target atom. Details of the Target atom are exactly copied from the PDB input file as shown here. A star * in column 6 marks an hetero-atom or H-bonding HYDrogen atom, just as it does in the input file GRINKOUT. Note that the table contains three rows (1184*, 1185* and 1186*) corresponding to hydrogen-bonding hydrogen atoms, and one row (1119*) corresponding to a water molecule which has been treated as a HETATM.
The final columns show the interaction energy between the Probe and each of the nearby Target atoms. Note that the interaction energy between the Probe and the 'HET' and 'HYD' atoms is not computed (see NETA above) although the HYDrogen atom still defines the direction of hydrogen bonding. The individual components of the energy are shown. The apparent discrepance between total energy values at the top (-4.7739) and the bottom (-4.56) of the table is due to Target atoms which are more distant from the Probe than the last tabulated atom (NH2 of ARG-5). A dummy value (-99.99) in the third line indicates that atom NH1 of ARG-5 is so close to the Probe that there would be a Lennard-Jones repulsion in the absence of hydrogen bonding. -99.99 in the last line of the table shows that the possibility of hydrogen-bonding between Probe and atom NH2 of ARG-5 was considered at an early stage of the computation. However it was rejected because the Probe (at this particular NX,NY,NZ) can accept two better hydrogen bonds from atoms NH1 and NE of the same residue.
CALCULATIONS FOR GRID PLANE NZ= 6 AT Z = 11.000
BEGIN WRITING RESULTS FOR THIS PLANE TO FILE
RESULTS FOR PLANE NZ= 6 HAVE ALL BEEN WRITTEN TO FILE
=======================================================
POINT E( 23, 37, 6) HAS -4.7739 KCAL/MOLE AT POSITION 15.000 ...
NEAREST ATOMS TO THIS MINIMUM ARE:-
1186* 46 HNH1 HYD 5 16.877 24.765 11.645 2.127
1184* 44 HNE HYD 5 15.814 23.088 12.912 2.269
46 46 NH1 ARG 5 17.577 24.823 12.357 0.00 0.00 3.40 3.027 3.00 2 0 0.192 0.00 -99.99 -2.03 -2.03
44 44 NE ARG 5 16.541 23.079 13.599 0.00 0.00 3.35 3.159 3.00 1 0 -0.029 0.00 -0.21 -1.88 -2.09
45 45 CZ ARG 5 17.530 23.993 13.418 0.00 0.00 3.50 3.500 0 0 0.460 0.00 -0.20 -0.20
1185* 46 HNH1 HYD 5 18.312 25.497 12.281 3.854
1119* 1119 OH2 NON 212 12.780 26.041 13.571 0.00 0.00 3.963
43 43 CD ARG 5 16.392 22.073 14.673 0.00 0.00 3.60 4.375 0 0 0.115 0.00 -0.10 -0.10
41 41 CB ARG 5 14.048 22.698 15.339 0.00 0.00 3.60 4.629 0 0 0.039 0.00 -0.08 -0.08
47 47 NH2 ARG 5 18.423 24.074 14.385 0.00 0.00 3.40 4.815 3.00 2 0 0.192 0.00 -0.06 -99.99 -0.06
COLUMN TOTALS:- 0.00 -0.64 -3.92 -4.56
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