Chapter 6-File formats

Pairing files.

The pairing file exists to specify the base pairing in cases where NAMOT2 is unable to determine the proper secondary structure. It also specifies the helical arrangements. This file is named by appending the basic file name with ".pair". (1BNA.full should have the pairing file:1BNA.pair; 1BNA should have the pairing file 1BNA.pair). The existence of this file overrides the automatic pairing routine.

The algorithm that searches for base pairing only works for standard Watson-Crick pairings. NAMOT2 WILL fail to pick the secondary structure on any unit with more than 2 bases.

The pairing information in the pairing file is arranged by helices. At the start of a new helix are two integers. The first is the number of units in this helix, the second is the number of bases per unit.

For each base in a unit, there is an entry that describes its position in the molecule:chain:group structure, its alpha face orientation, and whether or not Watson-Crick adjustment should be used to calculate the parameters. These are separated by colons. Alpha face is explained in the definitions sections.

Format:
<molecule #>:<chain #>:<group #>: <alpha face direction>:<Watson-Crick adjustment flag>

The M:C:G specifier will refer only to the molecule(s) being read in at that time. No information about the molecules that may or may not already exist in the program is needed.
If alpha face is up, then "1" is placed in that field, if not "2" is placed there.

If the parameters are to be Watson-Crick adjusted, then "wc" is placed in the final field, else "nwc" is placed there.

An example from the trna(trna04) pairing file:

7 2
1:1:1:1:wc 1:1:72:2:wc
1:1:2:1:wc 1:1:71:2:wc
1:1:3:1:wc 1:1:70:2:wc
1:1:4:1:wc 1:1:69:2:wc
1:1:5:1:wc 1:1:68:2:wc
1:1:6:1:wc 1:1:67:2:wc
1:1:7:1:wc 1:1:66:2:wc
2 1
1:1:8:1:wc
1:1:9:1:wc

PDB

AMBER

What NAMOT refers to as Amber is the pseudo-pdb output from Amber4.

Base library

This file contains the definition for the bases that NAMOT uses. NAMOT requires several bits of information besides the x,y,z coordinates. Note that "#" on the first column denotes a comment line.

<Names of bases>- This is a colon separated list of names that the base is known as.
<Number of atoms in base>
<Names of atoms in base>
<United Atom masses>-only the masses of the atoms used to determine base orientation should be specified, the rest should be zero.
<Index for vdw calculation>
<Atoms used to determine the alpha face. >
<Sign of Alpha face
<Ribose connection> <Base atom used to calculate Chi> <Base atom on other side of Ribose connection> These are used to calculate the glycosidic torsional and the position of C1*.
<XYZ>- In the moment of inertia frame.
<Connectivity>- In pdb format.

Example:

ADE:A:ADENINE
     14
     N1 C2 N3 C4 C5 C6 N7 C8 N9 N6 HN6A HN6B H2 H8
     14 13 14 12 12 12 14 13 14 0 0 0 0 0
     6 1 6 1 1 1 6 1 6 6 8 8 8 8
     N1 C2 N3
     +
     N9 C4 C8
1:N1 ade  -2.063495  -0.715351  -0.000114
2:C2 ade  -1.992841  0.613841  0.000237
3:N3 ade  -0.930903  1.390466  -0.000166
4:C4 ade  0.199861  0.654136  0.000333
5:C5 ade  0.286175  -0.707655  0.000396
6:C6 ade  -0.919782  -1.424797  -0.000354
7:N7 ade  1.614594  -1.110004  0.000032
8:C8 ade  2.279378  0.004041  -0.000002
9:N9 ade  1.485515  1.128271  -0.000292
10:N6     ade  -0.984498  -2.764497  -0.000143
11:HN6A   ade  -0.235619  -3.282948  -0.000667
12:HN6B   ade  -1.895456  -3.170218  -0.000276
13:H2     ade  -2.907653  1.017721  -0.000053
14:H8     ade  3.278658  0.041979  -0.000238
1       2       6
2       1       3   13
3       2       4
4       3       5       9
5       4       6       7
6       1       5       10
7       5       8
8       7       9   14
9       4       8
10      6       11      12
11      10
12      10
13   2
14   8

Phosphate library

This library defines the geometry of the phosphate group.

<Name of phosphate type>
<Number of atoms>
<United Atom Masses>
<Index for vdw contact calculation>
<fatm4 records for extensions off the normal phosphate>
- Three atoms that define the bond torsional,angle, and length. (The fourth atom is the # of the record )
- Bond length between atom 3 and atom 4.
- Angle between atom 2-atom3-atom 4
- Torsional angle.
<Connectivity in PDB format>

Example

#	1 = P
#	2 = O5'
#	4 = O2P
#	5 = S
#	
test
	4
	P S O2P H
	31 32 16 1
	7 4 4 8
# This describes the H which is the first non-standard atom.
	5 1 4 1.0 107 90
1	2	3
2	1
3	1	4
4	3

Sugar library

This library defines the geometry of the sugar group.

<Name of sugar>
<Number of atoms> <Number of off-ring atoms>
<Names of atoms>
<United Atom Masses>
<Index for vdw contact calculation>
<Records for off ring atoms>
- Four atoms that define the bond torsional,angle, and length,
- Bond length between atom 3 and atom 4.
- Angle between atom 2-atom3-atom 4
- Torsional angle.
<Connectivity in PDB format>

Example

deoxyribose
     12 7
     O4* C1* C2* C3* C4* O3* C5* O5* H2A* H2B* H3* H4*
     16 12 12 12 12 16 12 16 1 1 1 1
     4 1 1 1 1 4 1 4 8 8 8 8
# O3*
     5 3 4 6 1.43 109.5 120.0
# C5*
     1 4 5 7 1.53 109.5 240
# O5*
     1 5 7 8 1.427 109.5 120
# H2A*
     4 2 3 9 1.0  109.5  120
# H2B*
     4 2 3 10 1.0 109.5  240
# H3*
     5 3 4 11 1.0 109.5 240
# H4*
     1 2 5 12 1.0 109.5 120
1    2    5
2    1    3
3    2    4    9    10
4    3    5    6    11
5    1    4    7    12
6    4
7    5    8
8    7
9    2
10   2
11   4
12   5

Unit Library

This library defines the parameters for the units.

<Name of unit>
<Number of bases> <Watson Crick type for unit> (-1 is not a WC base).
Nucleoside info:
- <Base name> Alpha face direction <base type> <buckle> <opening> <propeller twist> <Sx> <Sy> <Sz>
- <Sugar name> <W> <q> <Chi>
- <Phosphate name> <C5'-O5'-P> <O5'-P-O3'> <Psuedorotational>

Example

at-nad
     2 -1
     ADE 1 -1 0 0 0 0 0 0
     deoxyribose  9.981689 0.359657 -150.036591
     phosphate 119.0 101.4 110.0
     THY 2 -1 0.046505 -28.879891 1.234555 2.483600 -5.454535 0.007036
     deoxyribose 10.039385 0.359698 -149.947647
     phosphate 119.0 101.4 110.0

Helix library

This file holds helices for the user. This can be used to store stem-loop structures.(They will be separate entries,though.)

<Number of units>
<Number of units> <Number of bases per unit>
<Strand directions>
<Inter-unit parameters>
<unit info>-The unit.lib entry that describes the unit. (This and the previous item are repeated for all units.)

#This helix(test2) was derived from:
#	THY ADE 
#	THY ADE 
test2
	2 2
	0 1 
	    0.000   -34.000     0.000    -0.000     0.000     3.400
	-
	2 -1
	THY 1 -1 0.00 -0.000 0.000 -0.000 0.000 0.000
	deoxyribose 10.012385 0.360195 -149.960617
	phosphate 0.000 0.000 0.000
	ADE 2 0 -0.052 -28.878 1.226 0.459 -5.975 0.024
	deoxyribose 9.935251 0.359547 -150.045898
	phosphate 101.000000 119.000000 0.00000
	    0.000   -34.000     0.000    -0.000     0.000     3.400
	-
	2 -1
	THY 1 -1 0.000 -0.000 0.000 -0.000 0.000 0.000
	deoxyribose 10.012385 0.360195 -149.960617
	normal 101.000000 119.000000 0.000000
	ADE 2 0 -0.052 -28.878 1.226 0.459 -5.975 0.024
	deoxyribose 9.935251 0.359547 -150.045898
	normal 0.000000 0.000000 0.000000

Form Library

This file holds the parameters for different helical forms. When a unit is chosen or the form type is changed, NAMOT2 will place the inter-unit parameters in the proper fields of the add unit popup. When a user adds a unit, the program will look to see if the unit is in the library, if it is in the library, it will use the unit library record in the form library to set the intra-unit parameters as well as the sugar and phosphate records. If the unit is not specified for that form, then it will use the the unknown ("unk") record to set the sugar and phosphate values only.

<Form name> <number of units in the record>
<Unit name> Dx Dy Dz Tilt Twist Roll
<Unit record as described above>

Z 5
#
	gc-nad -0.657    5.319   -3.46  -2.350   22.218   -5.923 
	-
	2 -1
	- 1 -1 0 0 0 0 0 0
     deoxyribose 0.003705 0.239998 66.001030
	phosphate  101 119 153.3
	- 2 -1 -0.022   41.067   -0.845    3.245   -4.427   -0.046
	deoxyribose 154.001938 0.339999 -160.031357
	phosphate  101 119 153.3
#
	gc-wc -0.679    5.090   -3.467 -2.350   23.466   -5.616
	-
	2 -1
	- 1 -1 0 0 0 0 0 0
     deoxyribose 0.003705 0.239998 66.001030
	phosphate  101 119 153.3
 	- 2 -1 0.0 -0.0 0.0 0.0 -0.00 0.00
	deoxyribose 154.001938 0.339999 -160.031357
	phosphate  101 119 153.3
#
	cg-nad  0.602   -1.613   -3.631 0.149   36.550   -0.101
	-
	2 -1
	- 1 -1 0 0 0 0 0 0
	deoxyribose  154 0.34 -160.0
	phosphate       80 100 116.0
	- 2 -1 -0.042   41.029   -0.850    0.458   -5.470   -0.025
     deoxyribose -0.002094 0.240201 66.044975
	phosphate       80 100 116.0
#
	cg-wc  0.515   -1.369   -3.626 0.149   35.299   -0.411
	-
	2 -1
	- 1 -1 0 0 0 0 0 0
	deoxyribose  154 0.34 -160.0
	phosphate       80 100 116.0
 	- 2 -1 0.00 0.00 0.00 0.00 0.00 0.00
     deoxyribose -0.002094 0.240201 66.044975
	phosphate       80 100 116.0
#
	unk 0.57 -1.6 -3.63 0.0 40.0 0.57
	-
	2 -1
	- 1 -1 0 0 0 0 0 0
	deoxyribose  9.981689 0.359657 -150.036591 
	phosphate  101 119 153.3
 	- 2 -1 0.046505 -28.879891 1.234555 2.483600 -5.454535 0.007036
	deoxyribose 10.039385 0.359698 -149.947647 
	phosphate  101 119 153.3

Parameter file format

This format is used to input and output structures in the reduced coordinate set. It is largely drawn from the other format methods.

"SEQUENCE"
<sequence>
This is the primary sequence information. Only ten residues should appear on a line. Each chain is terminated by a "TER" record. Molecules are separated by "ENDMDL". The final molecule should not end with "ENDMDL". The "ENDMDL" should appear on a line by itself.
"PAIRING"
<pairing records>
This format is described above.
"PARAMETERS"
<Helix records>
This format is the same as the helix library format

Example:

SEQUENCE
ADE ADE TER
THY THY TER
PAIRING
2 2
        1:1:1:1:nwc 1:2:2:2:nwc 
        1:1:2:1:nwc 1:2:1:2:nwc 
PARAMETERS
-
2 2
        0 1 
            0.000  -34.000    0.000   -0.000    0.000    3.400
        -
                2 -1
                ADE 1 -1    0.000  -0.000   0.000  -0.000   0.000   0.000
                deoxyribose  160.000   0.360 -90.000
                phosphate  119.000 101.400 160.000
                THY 2 0    0.047 -28.880   1.235   2.484  -5.455   0.007
                deoxyribose  160.000   0.360 -90.000
                phosphate  119.000 101.400 160.000
            0.000  -34.000    0.000   -0.000    0.000    3.400
        -
                2 -1
                ADE 1 -1    0.000  -0.000   0.000  -0.000   0.000   0.000
                deoxyribose  160.000   0.360 -90.000
                phosphate  119.000 101.400 160.000
                THY 2 0    0.047 -28.880   1.235   2.484  -5.455   0.007
                deoxyribose  160.000   0.360 -90.000
                phosphate  119.000 101.400 160.000

VDW library

This library holds the VDW radii for the different types of atoms.

<Number of atom types>
<Entries>
- <Atom type> <radius>
  The Atom type field is ignored, it exists for human readablity.

Example:

8
c         1.850 
c2        1.925
c3        2.000
o         1.600
os        1.650
n         1.750
p         2.100
h         1.000