[gromacs.git] / src / gromacs / gmxpreprocess / tests / refdata / ChainChanges_Pdb2gmxTest_ProducesMatchingTopology_0.xml
| blob | 5489194072dc8a30a4af83a87b5db5cdebe6a0a5 |
1 <?xml version="1.0"?>
2 <?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
3 <ReferenceData>
4 <OutputFiles Name="Files">
5 <File Name="-o">
6 <String Name="Contents"><![CDATA[
7 TITLE Fragments of peptides and ions
8 REMARK THIS IS A SIMULATION BOX
9 CRYST1 80.562 56.371 74.450 90.00 90.00 90.00 P 1 1
10 MODEL 1
11 ATOM 1 N ALA A 2 43.810 17.900 -0.540 1.00 0.00 N
12 ATOM 2 H1 ALA A 2 44.800 17.785 -0.622 1.00 0.00
13 ATOM 3 H2 ALA A 2 43.377 17.004 -0.438 1.00 0.00
14 ATOM 4 H3 ALA A 2 43.458 18.349 -1.362 1.00 0.00
15 ATOM 5 CA ALA A 2 43.500 18.750 0.670 1.00 0.00 C
16 ATOM 6 HA ALA A 2 43.728 18.142 1.430 1.00 0.00
17 ATOM 7 CB ALA A 2 44.390 20.060 0.730 1.00 0.00 C
18 ATOM 8 HB1 ALA A 2 44.150 20.589 1.544 1.00 0.00
19 ATOM 9 HB2 ALA A 2 45.356 19.805 0.770 1.00 0.00
20 ATOM 10 HB3 ALA A 2 44.225 20.613 -0.087 1.00 0.00
21 ATOM 11 C ALA A 2 42.030 19.010 0.920 1.00 0.00 C
22 ATOM 12 O ALA A 2 41.550 18.760 2.010 1.00 0.00 O
23 ATOM 13 N CYS A 3 41.410 19.640 -0.130 1.00 0.00 N
24 ATOM 14 HN CYS A 3 41.928 19.877 -0.952 1.00 0.00
25 ATOM 15 CA CYS A 3 40.000 19.960 -0.040 1.00 0.00 C
26 ATOM 16 HA CYS A 3 39.726 19.549 0.830 1.00 0.00
27 ATOM 17 CB CYS A 3 39.690 21.510 -0.040 1.00 0.00 C
28 ATOM 18 HB1 CYS A 3 40.088 21.896 -0.872 1.00 0.00
29 ATOM 19 HB2 CYS A 3 38.696 21.618 -0.065 1.00 0.00
30 ATOM 20 SG CYS A 3 40.430 22.190 1.470 1.00 0.00 S
31 ATOM 21 HG1 CYS A 3 40.257 23.174 1.512 1.00 0.00
32 ATOM 22 C CYS A 3 39.300 19.330 -1.220 1.00 0.00 C
33 ATOM 23 O CYS A 3 38.170 19.680 -1.550 1.00 0.00 O
34 ATOM 24 N ASP A 4 40.000 18.460 -1.980 1.00 0.00 N
35 ATOM 25 HN ASP A 4 40.969 18.366 -1.751 1.00 0.00
36 ATOM 26 CA ASP A 4 39.530 17.640 -3.090 1.00 0.00 C
37 ATOM 27 HA ASP A 4 39.109 18.223 -3.785 1.00 0.00
38 ATOM 28 CB ASP A 4 40.780 16.940 -3.740 1.00 0.00 C
39 ATOM 29 HB1 ASP A 4 40.501 16.361 -4.506 1.00 0.00
40 ATOM 30 HB2 ASP A 4 41.439 17.621 -4.059 1.00 0.00
41 ATOM 31 CG ASP A 4 41.430 16.080 -2.680 1.00 0.00 C
42 ATOM 32 OD1 ASP A 4 41.220 14.850 -2.810 1.00 0.00 O
43 ATOM 33 OD2 ASP A 4 41.940 16.580 -1.630 1.00 0.00 O
44 ATOM 34 C ASP A 4 38.410 16.690 -2.560 1.00 0.00 C
45 ATOM 35 OT1 ASP A 4 37.470 17.010 -1.820 1.00 0.00 O
46 ATOM 36 OT2 ASP A 4 37.844 15.841 -3.459 1.00 0.00
47 ATOM 37 N THR B 18 47.530 15.820 0.820 1.00 0.00 N
48 ATOM 38 H1 THR B 18 47.507 16.562 1.490 1.00 0.00
49 ATOM 39 H2 THR B 18 46.700 15.269 0.904 1.00 0.00
50 ATOM 40 H3 THR B 18 48.330 15.244 0.987 1.00 0.00
51 ATOM 41 CA THR B 18 47.610 16.400 -0.570 1.00 0.00 C
52 ATOM 42 HA THR B 18 46.749 16.906 -0.523 1.00 0.00
53 ATOM 43 CB THR B 18 48.740 17.360 -0.930 1.00 0.00 C
54 ATOM 44 HB THR B 18 48.898 17.421 -1.916 1.00 0.00
55 ATOM 45 OG1 THR B 18 50.020 16.940 -0.390 1.00 0.00 O
56 ATOM 46 HG1 THR B 18 50.725 17.599 -0.652 1.00 0.00
57 ATOM 47 CG2 THR B 18 48.330 18.640 -0.210 1.00 0.00 C
58 ATOM 48 HG21 THR B 18 49.012 19.351 -0.380 1.00 0.00
59 ATOM 49 HG22 THR B 18 47.440 18.944 -0.551 1.00 0.00
60 ATOM 50 HG23 THR B 18 48.269 18.465 0.773 1.00 0.00
61 ATOM 51 C THR B 18 47.650 15.380 -1.660 1.00 0.00 C
62 ATOM 52 O THR B 18 48.350 14.370 -1.570 1.00 0.00 O
63 ATOM 53 N VAL B 19 46.990 15.650 -2.800 1.00 0.00 N
64 ATOM 54 HN VAL B 19 46.589 16.555 -2.944 1.00 0.00
65 ATOM 55 CA VAL B 19 46.860 14.630 -3.820 1.00 0.00 C
66 ATOM 56 HA VAL B 19 46.794 13.844 -3.206 1.00 0.00
67 ATOM 57 CB VAL B 19 45.590 14.650 -4.650 1.00 0.00 C
68 ATOM 58 HB VAL B 19 45.844 14.046 -5.405 1.00 0.00
69 ATOM 59 CG1 VAL B 19 44.330 14.240 -3.760 1.00 0.00 C
70 ATOM 60 HG11 VAL B 19 43.504 14.259 -4.323 1.00 0.00
71 ATOM 61 HG12 VAL B 19 44.465 13.318 -3.396 1.00 0.00
72 ATOM 62 HG13 VAL B 19 44.232 14.886 -3.003 1.00 0.00
73 ATOM 63 CG2 VAL B 19 45.210 15.960 -5.270 1.00 0.00 C
74 ATOM 64 HG21 VAL B 19 44.362 15.850 -5.789 1.00 0.00
75 ATOM 65 HG22 VAL B 19 45.075 16.642 -4.551 1.00 0.00
76 ATOM 66 HG23 VAL B 19 45.939 16.262 -5.884 1.00 0.00
77 ATOM 67 C VAL B 19 48.080 14.550 -4.760 1.00 0.00 C
78 ATOM 68 O VAL B 19 48.100 13.660 -5.600 1.00 0.00 O
79 ATOM 69 N TRP B 20 49.000 15.510 -4.590 1.00 0.00 N
80 ATOM 70 HN TRP B 20 48.796 16.221 -3.917 1.00 0.00
81 ATOM 71 CA TRP B 20 50.240 15.610 -5.280 1.00 0.00 C
82 ATOM 72 HA TRP B 20 50.610 14.686 -5.379 1.00 0.00
83 ATOM 73 CB TRP B 20 50.000 16.290 -6.650 1.00 0.00 C
84 ATOM 74 HB1 TRP B 20 49.286 15.797 -7.147 1.00 0.00
85 ATOM 75 HB2 TRP B 20 49.713 17.237 -6.507 1.00 0.00
86 ATOM 76 CG TRP B 20 51.260 16.290 -7.490 1.00 0.00 C
87 ATOM 77 CD1 TRP B 20 51.940 15.180 -7.930 1.00 0.00 C
88 ATOM 78 HD1 TRP B 20 51.756 14.257 -7.592 1.00 0.00
89 ATOM 79 NE1 TRP B 20 52.910 15.460 -8.890 1.00 0.00 N
90 ATOM 80 HE1 TRP B 20 53.500 14.803 -9.358 1.00 0.00
91 ATOM 81 CE2 TRP B 20 52.890 16.880 -9.070 1.00 0.00 C
92 ATOM 82 CD2 TRP B 20 51.790 17.380 -8.290 1.00 0.00 C
93 ATOM 83 CE3 TRP B 20 51.560 18.780 -8.300 1.00 0.00 C
94 ATOM 84 HE3 TRP B 20 50.849 19.172 -7.717 1.00 0.00
95 ATOM 85 CZ3 TRP B 20 52.340 19.630 -9.140 1.00 0.00 C
96 ATOM 86 HZ3 TRP B 20 52.140 20.608 -9.198 1.00 0.00
97 ATOM 87 CZ2 TRP B 20 53.670 17.750 -9.810 1.00 0.00 C
98 ATOM 88 HZ2 TRP B 20 54.463 17.404 -10.311 1.00 0.00
99 ATOM 89 CH2 TRP B 20 53.360 19.090 -9.860 1.00 0.00 C
100 ATOM 90 HH2 TRP B 20 53.905 19.689 -10.447 1.00 0.00
101 ATOM 91 C TRP B 20 51.120 16.530 -4.440 1.00 0.00 C
102 ATOM 92 OT1 TRP B 20 50.690 16.980 -3.420 1.00 0.00 O
103 ATOM 93 OT2 TRP B 20 52.373 16.779 -4.905 1.00 0.00
104 TER
105 ENDMDL
106 ]]></String>
107 </File>
108 <File Name="-p">
109 <String Name="Contents"><![CDATA[
110 ;
111 ;
112 ; This is a standalone topology file
113 ;
114 ; Created by:
115 ;
116 ; Command line:
117 ; Force field was read from the standard GROMACS share directory.
118 ;
120 ; Include forcefield parameters
121 #include "charmm27.ff/forcefield.itp"
123 ; Include chain topologies
124 #include "ChainChanges_Pdb2gmxTest_ProducesMatchingTopology_0_topol_Protein_chain_A.itp"
125 #include "ChainChanges_Pdb2gmxTest_ProducesMatchingTopology_0_topol_Protein_chain_B.itp"
127 ; Include water topology
128 #include "charmm27.ff/tip3p.itp"
130 #ifdef POSRES_WATER
131 ; Position restraint for each water oxygen
132 [ position_restraints ]
133 ; i funct fcx fcy fcz
134 1 1 1000 1000 1000
135 #endif
137 ; Include topology for ions
138 #include "charmm27.ff/ions.itp"
140 [ system ]
141 ; Name
142 Fragments of peptides and ions
144 [ molecules ]
145 ; Compound #mols
146 Protein_chain_A 1
147 Protein_chain_B 1
148 ]]></String>
149 </File>
150 </OutputFiles>
151 </ReferenceData>