Suppose the coordinates look like:
ATOM 6061 C1 NAG J 100 35.115 45.254 26.962 1.00 80.61 J ATOM 6062 O1 NAG J 100 35.377 46.459 26.322 1.00 82.53 J ATOM 6063 C2 NAG J 100 33.914 45.427 27.904 1.00 79.68 J ATOM 6064 N2 NAG J 100 34.342 46.212 29.048 1.00 76.74 J ATOM 6065 C7 NAG J 100 33.703 47.331 29.391 1.00 77.06 J ATOM 6066 O7 NAG J 100 32.759 47.811 28.741 1.00 73.53 J ATOM 6067 C8 NAG J 100 34.194 48.023 30.661 1.00 75.36 J ATOM 6068 C3 NAG J 100 33.328 44.080 28.404 1.00 79.56 J ATOM 6069 O3 NAG J 100 32.006 44.297 28.880 1.00 76.89 J ATOM 6070 C4 NAG J 100 33.288 42.978 27.322 1.00 80.90 J ATOM 6071 O4 NAG J 100 33.117 41.684 27.949 1.00 81.05 J ATOM 6072 C5 NAG J 100 34.596 42.967 26.526 1.00 82.74 J ATOM 6073 O5 NAG J 100 34.836 44.274 25.957 1.00 81.58 J ATOM 6074 C6 NAG J 100 34.610 41.950 25.387 1.00 83.21 J ATOM 6075 O6 NAG J 100 33.690 42.295 24.361 1.00 84.17 J |
Then the topology that Prodrug makes will look like:
* NAG 1 # AT BND CHI TRS CRD #BL HGR HAT ANG 1-3 PAR PC HANG TYP 20 20 7 7 1 20 0 15 27 1 1 1 21 6 #===== Atom names C8 C7 O7 N2 HAE C2 C3 O3 HAB C4 O4 HAC C5 C6 O6 HAD O5 C1 O1 HAA #===== Bonds 1 2 2 3 2 4 4 5 4 6 6 7 6 18 7 8 7 10 8 9 10 11 10 13 11 12 13 14 13 17 14 15 15 16 17 18 18 19 19 20 #===== Rotatable bonds 2 4 1 3 4 6 1 2 3 5 7 8 9 10 11 12 13 14 15 16 14 15 16 18 19 20 #===== Torsion angles 1 2 4 6 2 4 6 18 6 7 8 9 7 10 11 12 10 13 14 15 13 14 15 16 6 18 19 20 #===== Coordinates, hydrogen bonding and planarity 46.49850 48.65450 47.73000 F 45.62850 47.97450 46.67000 F 44.68850 48.57450 46.15000 T- 45.96850 46.72450 46.38000 T+ 2 46.73850 46.25450 46.82999 F 45.25850 45.90450 45.39000 F 44.53850 44.73450 46.07000 F 43.51850 45.25449 46.93000 T 4 43.01850 44.50450 47.36000 F 43.87850 43.81450 45.04000 F 43.34850 42.66450 45.71999 T 4 42.89850 42.06450 45.06000 F 44.91850 43.36450 44.00000 F 44.24850 42.53450 42.89000 F 45.23850 42.08450 41.96000 T 4 44.79850 41.54450 41.24000 F 45.54850 44.52450 43.39000 T- 46.24850 45.36450 44.34000 F 46.85850 46.45450 43.65000 T 4 46.15850 47.00450 43.20000 F #===== Standard bond lengths 1.530 0.020 1.230 0.020 1.330 0.020 1.000 0.020 1.470 0.020 1.530 0.020 1.530 0.020 1.430 0.020 1.530 0.020 1.000 0.020 1.430 0.020 1.530 0.020 1.000 0.020 1.530 0.020 1.435 0.020 1.430 0.020 1.000 0.020 1.435 0.020 1.430 0.020 1.000 0.020 #===== Standard bond angles 1 2 3 121.0 2.0 1 2 4 115.0 2.0 3 2 4 124.0 2.0 2 4 6 122.0 2.0 4 6 7 109.5 2.0 4 6 18 109.5 2.0 7 6 18 111.0 2.0 6 7 8 109.5 2.0 6 7 10 111.0 2.0 8 7 10 109.5 2.0 7 10 11 109.5 2.0 7 10 13 111.0 2.0 11 10 13 109.5 2.0 10 13 14 109.5 2.0 10 13 17 109.5 2.0 14 13 17 109.5 2.0 13 14 15 109.5 2.0 13 17 18 109.5 2.0 6 18 17 109.5 2.0 6 18 19 109.5 2.0 17 18 19 109.5 2.0 2 4 5 123.0 2.0 5 4 6 115.0 2.0 7 8 9 109.5 2.0 10 11 12 109.5 2.0 14 15 16 109.5 2.0 18 19 20 109.5 2.0 3 3 4 3 5 6 3 1 4 5 1 3 7 18 3 2 6 7 2 5 8 10 17 19 6 4 18 9 11 13 3 6 10 2 7 6 6 8 12 14 17 3 7 13 2 10 5 7 11 15 18 4 10 17 16 2 13 2 14 5 10 14 6 19 5 4 7 13 20 3 6 17 2 18 #===== Charges 0.017 0.219 -0.420 0.082 0.003 0.077 0.077 -0.112 0.031 0.077 -0.112 0.031 0.130 0.039 -0.112 0.031 -0.107 0.130 -0.112 0.031 *END |
And the annotation of all the lines and colums is given in the box below:
Per amino acid the following information is given:
1) An asterisk
2) The name in 3 and 1 letter code (A4,A1 left justified)
3) Some constants that indicate: (Free format integers)
1) The number of atoms (ATPRAA)
2) The number of intra-residue bonds
3) The number of rotable side-chain torsion angles (CHIUSE)
4) The number of measurable torsion angles
5) 1 -> Standard atomic coordinates are present ( 0 -> not )
6) Standard bondlengths for the first N bonds
7) Number of hydrogen bond 'groups'
8) Number of non-protons in residue
9) Number of bond angles given
10) 1 -> 1/3 connections for all atoms are given ( 0 -> not )
11) Number of atomic parameter sets per class (max : 4)
12) Number of atomic parameter classes (max : 2)
13) Number of angles given under 9 that do not include protons
14) Residue family type
1 = protein
3 = nucleic acid
6 = co-factor with topology
15) Number of sets of atom names
4) The atom names (14A4 left justified)
5) Pairs of bonded atoms (10 pairs of integers per line, free format)
6) Per rotatable side-chain: the two atoms that define the axis followed
by all atoms that should rotate (20 integers per line, free format)
7) Per measurable torsion angle the four atoms (20 free format
integers per line; that is 5 torsion angles per line)
8) Per atom the following information:
1) Standard X coordinate \
2) Standard Y coordinate |-> free formatted within columns 1-29
3) Standard Z coordinate /
4) T or F for hydrogen bondable or not. Fixed in column 30.
5) + or - for donor or acceptor (blank means both possible) Fixed
in column 31
6) Hydrogen bond type number. Fixed column 33.
1) N-H on backbone of protein
2) N-H in sidechain of ARG and TRP and D/RNA
3) N-H2
4) O-H (SER, THR, TYR) [Rotatable by HB2]
5) N-H3 (LYS)
6) N-H that is sometimes absent (HIS)
7) O-H that is sometimes present (ASP, GLU)
7) Group number this donor/acceptor is member of. Fixed column 35.
8) The planes this atom is part of. Columns 36-39.
9) The standard bondlengths with sigma (one per line, free format)
10) Bond angles with sigma, preceded by numbers of the atoms making the bond
11) Per atom number of 1-3 bonded atoms (plus 1) and those atoms
12) One line for each hydrogen bond group (I5,30F5.2):
1) Number of atoms in the hydrogen group
2) Penalties for having 0...N hydrogens in the group.
13) Param(11) Param(12) lines with atomic parameter values
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I guess you should just be glad that you normally don't have to worry about these problems.