read-watbox.str

Posted by: lennart

read-watbox.str - 08/17/04 03:44 AM

This needs to be correctly formatted. If you get it by cut&paste just get everything between the lines.
code:

*FILENAME: read-watbox.str
*PURPOSE: read 216 water molecule coord; used in solvation scripts
*AUTHOR: Lennart Nilsson, Karolinska Institutet, October 2003
read coor card resid
* This is a box of 216 3-site water molecules in the experimental
* geometry. It was constructed from an equilibrated
* configuration of TIP4P (4-site water model of Jorgenson)
* waters at 1 atm pressure and a density of 0.0334 molecules/A**-3.
* The box edgelength is 18.856 A. The minimum image periodic
* boundary energy for this configuration using the TIP4P
* potentials is -2150.6833 kcal/mol.
*
648
1 1 TIP3 OH2 2.53067 0.59634 -2.47655 WAT0 1 0.00000
2 1 TIP3 H1 2.61978 1.54016 -2.60884 WAT0 1 0.00000
3 1 TIP3 H2 1.89243 0.32098 -3.13461 WAT0 1 0.00000
4 2 TIP3 OH2 1.46380 -0.14859 0.94227 WAT0 2 0.00000
5 2 TIP3 H1 1.42555 -0.79496 1.64723 WAT0 2 0.00000
6 2 TIP3 H2 1.14145 -0.61515 0.17114 WAT0 2 0.00000
7 3 TIP3 OH2 -6.16770 -0.53438 2.53526 WAT0 3 0.00000
8 3 TIP3 H1 -6.12649 -1.16005 3.25850 WAT0 3 0.00000
9 3 TIP3 H2 -5.46493 0.08948 2.71730 WAT0 3 0.00000
10 4 TIP3 OH2 5.16982 2.79045 -0.75622 WAT0 4 0.00000
11 4 TIP3 H1 4.72909 2.07005 -0.30566 WAT0 4 0.00000
12 4 TIP3 H2 5.15679 3.51117 -0.12645 WAT0 4 0.00000
13 5 TIP3 OH2 -5.24439 3.91551 1.07017 WAT0 5 0.00000
14 5 TIP3 H1 -5.61387 3.11356 0.70060 WAT0 5 0.00000
15 5 TIP3 H2 -4.30328 3.74700 1.11651 WAT0 5 0.00000
16 6 TIP3 OH2 -8.63434 -2.42423 -3.53695 WAT0 6 0.00000
17 6 TIP3 H1 -9.08200 -1.57836 -3.55530 WAT0 6 0.00000
18 6 TIP3 H2 -9.19522 -3.00381 -4.05244 WAT0 6 0.00000
19 7 TIP3 OH2 -7.92373 -0.26227 -1.41115 WAT0 7 0.00000
20 7 TIP3 H1 -7.71038 -1.03211 -0.88385 WAT0 7 0.00000
21 7 TIP3 H2 -7.18597 -0.17260 -2.01439 WAT0 7 0.00000
22 8 TIP3 OH2 2.28137 7.89462 -0.54418 WAT0 8 0.00000
23 8 TIP3 H1 2.90101 7.21809 -0.81726 WAT0 8 0.00000
24 8 TIP3 H2 2.07311 7.67670 0.36431 WAT0 8 0.00000
25 9 TIP3 OH2 -0.14676 2.28355 1.34837 WAT0 9 0.00000
26 9 TIP3 H1 0.15703 1.59769 0.75378 WAT0 9 0.00000
27 9 TIP3 H2 0.57464 2.40242 1.96617 WAT0 9 0.00000
28 10 TIP3 OH2 8.51622 -6.11492 2.20899 WAT0 10 0.00000
29 10 TIP3 H1 8.56544 -5.50480 2.94490 WAT0 10 0.00000
30 10 TIP3 H2 8.94173 -5.65383 1.48610 WAT0 10 0.00000
31 11 TIP3 OH2 2.99394 -3.32221 1.67585 WAT0 11 0.00000
32 11 TIP3 H1 3.13653 -4.26851 1.69601 WAT0 11 0.00000
33 11 TIP3 H2 2.88784 -3.11523 0.74734 WAT0 11 0.00000
34 12 TIP3 OH2 -3.85123 -5.22057 -1.05167 WAT0 12 0.00000
35 12 TIP3 H1 -3.80812 -4.36072 -1.47004 WAT0 12 0.00000
36 12 TIP3 H2 -4.30882 -5.77310 -1.68535 WAT0 12 0.00000
37 13 TIP3 OH2 3.87104 -5.09001 -2.65084 WAT0 13 0.00000
38 13 TIP3 H1 4.51747 -5.41869 -2.02608 WAT0 13 0.00000
39 13 TIP3 H2 4.38098 -4.57211 -3.27370 WAT0 13 0.00000
40 14 TIP3 OH2 -7.23108 -2.82399 -0.28953 WAT0 14 0.00000
41 14 TIP3 H1 -6.57742 -3.37382 0.14248 WAT0 14 0.00000
42 14 TIP3 H2 -7.20715 -3.09809 -1.20633 WAT0 14 0.00000
43 15 TIP3 OH2 -2.07463 -1.27386 -1.07438 WAT0 15 0.00000
44 15 TIP3 H1 -1.45853 -1.80032 -0.56498 WAT0 15 0.00000
45 15 TIP3 H2 -2.66075 -1.91399 -1.47802 WAT0 15 0.00000
46 16 TIP3 OH2 8.90768 -4.63700 4.44497 WAT0 16 0.00000
47 16 TIP3 H1 8.21914 -3.97893 4.34963 WAT0 16 0.00000
48 16 TIP3 H2 8.92314 -4.83421 5.38151 WAT0 16 0.00000
49 17 TIP3 OH2 -5.04104 -6.30273 3.02241 WAT0 17 0.00000
50 17 TIP3 H1 -5.25987 -5.77267 2.25601 WAT0 17 0.00000
51 17 TIP3 H2 -5.70895 -6.07618 3.66955 WAT0 17 0.00000
52 18 TIP3 OH2 2.32794 3.19738 -3.43368 WAT0 18 0.00000
53 18 TIP3 H1 2.03245 2.87461 -4.28499 WAT0 18 0.00000
54 18 TIP3 H2 2.00372 4.09705 -3.39242 WAT0 18 0.00000
55 19 TIP3 OH2 -2.47190 1.37284 3.30978 WAT0 19 0.00000
56 19 TIP3 H1 -3.21199 1.97099 3.41330 WAT0 19 0.00000
57 19 TIP3 H2 -1.75795 1.92680 2.99414 WAT0 19 0.00000
58 20 TIP3 OH2 5.63488 -5.79908 -0.67025 WAT0 20 0.00000
59 20 TIP3 H1 5.41968 -6.56474 -0.13765 WAT0 20 0.00000
60 20 TIP3 H2 6.29062 -5.32662 -0.15740 WAT0 20 0.00000
61 21 TIP3 OH2 -5.44731 -4.41055 0.97463 WAT0 21 0.00000
62 21 TIP3 H1 -4.83368 -3.77779 1.34787 WAT0 21 0.00000
63 21 TIP3 H2 -4.93524 -4.88305 0.31832 WAT0 21 0.00000
64 22 TIP3 OH2 -4.06447 3.33714 4.09693 WAT0 22 0.00000
65 22 TIP3 H1 -4.06971 4.21649 3.71886 WAT0 22 0.00000
66 22 TIP3 H2 -4.91806 3.25355 4.52192 WAT0 22 0.00000
67 23 TIP3 OH2 -7.94338 3.00793 -5.12114 WAT0 23 0.00000
68 23 TIP3 H1 -8.21529 3.23703 -6.00985 WAT0 23 0.00000
69 23 TIP3 H2 -7.89781 3.84581 -4.66061 WAT0 23 0.00000
70 24 TIP3 OH2 5.68159 4.62952 1.59171 WAT0 24 0.00000
71 24 TIP3 H1 4.73996 4.68791 1.75340 WAT0 24 0.00000
72 24 TIP3 H2 5.95820 5.53557 1.45468 WAT0 24 0.00000
73 25 TIP3 OH2 5.98229 -7.08395 3.00910 WAT0 25 0.00000
74 25 TIP3 H1 5.24621 -6.47324 2.97123 WAT0 25 0.00000
75 25 TIP3 H2 6.66569 -6.66905 2.48274 WAT0 25 0.00000
76 26 TIP3 OH2 -1.01457 -8.99722 0.47490 WAT0 26 0.00000
77 26 TIP3 H1 -1.13215 -9.94562 0.42073 WAT0 26 0.00000
78 26 TIP3 H2 -1.86956 -8.66461 0.74801 WAT0 26 0.00000
79 27 TIP3 OH2 3.93371 6.41087 -1.78313 WAT0 27 0.00000
80 27 TIP3 H1 4.35894 5.70366 -2.26817 WAT0 27 0.00000
81 27 TIP3 H2 4.25071 7.21214 -2.19991 WAT0 27 0.00000
82 28 TIP3 OH2 5.09336 4.31172 -3.27447 WAT0 28 0.00000
83 28 TIP3 H1 4.83584 3.62173 -3.88588 WAT0 28 0.00000
84 28 TIP3 H2 5.16444 3.86884 -2.42888 WAT0 28 0.00000
85 29 TIP3 OH2 6.77938 2.87839 5.20288 WAT0 29 0.00000
86 29 TIP3 H1 6.91901 2.28664 4.46358 WAT0 29 0.00000
87 29 TIP3 H2 6.94666 3.75098 4.84676 WAT0 29 0.00000
88 30 TIP3 OH2 1.25192 -0.15966 -5.02452 WAT0 30 0.00000
89 30 TIP3 H1 0.54047 0.37531 -5.37647 WAT0 30 0.00000
90 30 TIP3 H2 1.94288 -0.10445 -5.68463 WAT0 30 0.00000
91 31 TIP3 OH2 1.30584 -1.70223 -7.98602 WAT0 31 0.00000
92 31 TIP3 H1 2.00683 -1.67954 -7.33462 WAT0 31 0.00000
93 31 TIP3 H2 1.60813 -2.33026 -8.64209 WAT0 31 0.00000
94 32 TIP3 OH2 8.62131 -0.78181 3.26892 WAT0 32 0.00000
95 32 TIP3 H1 7.96872 -0.08725 3.35801 WAT0 32 0.00000
96 32 TIP3 H2 9.08634 -0.57172 2.45908 WAT0 32 0.00000
97 33 TIP3 OH2 4.65769 0.04967 -4.07293 WAT0 33 0.00000
98 33 TIP3 H1 3.92579 0.27804 -3.49987 WAT0 33 0.00000
99 33 TIP3 H2 5.10491 -0.66406 -3.61818 WAT0 33 0.00000
100 34 TIP3 OH2 4.55504 -1.77607 4.99477 WAT0 34 0.00000
101 34 TIP3 H1 4.63495 -1.01263 5.56662 WAT0 34 0.00000
102 34 TIP3 H2 3.95381 -1.49683 4.30428 WAT0 34 0.00000
103 35 TIP3 OH2 -3.69694 0.68029 -2.19043 WAT0 35 0.00000
104 35 TIP3 H1 -4.02742 0.30963 -3.00873 WAT0 35 0.00000
105 35 TIP3 H2 -3.10853 0.00969 -1.84360 WAT0 35 0.00000
106 36 TIP3 OH2 -2.33019 4.10835 0.49079 WAT0 36 0.00000
107 36 TIP3 H1 -2.42506 3.52966 -0.26575 WAT0 36 0.00000
108 36 TIP3 H2 -1.60083 3.73692 0.98707 WAT0 36 0.00000
109 37 TIP3 OH2 -3.33039 -0.55115 1.44307 WAT0 37 0.00000
110 37 TIP3 H1 -2.76514 -0.42973 0.68019 WAT0 37 0.00000
111 37 TIP3 H2 -3.01150 0.08635 2.08192 WAT0 37 0.00000
112 38 TIP3 OH2 2.97883 4.95204 2.17712 WAT0 38 0.00000
113 38 TIP3 H1 2.73849 5.61435 2.82504 WAT0 38 0.00000
114 38 TIP3 H2 2.78065 4.11756 2.60208 WAT0 38 0.00000
115 39 TIP3 OH2 -2.45032 3.84812 6.16026 WAT0 39 0.00000
116 39 TIP3 H1 -2.76157 4.63044 6.61558 WAT0 39 0.00000
117 39 TIP3 H2 -3.10030 3.69503 5.47446 WAT0 39 0.00000
118 40 TIP3 OH2 3.52864 -0.78804 -6.38781 WAT0 40 0.00000
119 40 TIP3 H1 4.10819 -0.63801 -5.64092 WAT0 40 0.00000
120 40 TIP3 H2 3.94264 -0.31730 -7.11117 WAT0 40 0.00000
121 41 TIP3 OH2 -5.53033 0.04623 5.38883 WAT0 41 0.00000
122 41 TIP3 H1 -5.46001 0.69691 6.08733 WAT0 41 0.00000
123 41 TIP3 H2 -6.42111 0.14898 5.05392 WAT0 41 0.00000
124 42 TIP3 OH2 1.25513 5.94881 -2.95250 WAT0 42 0.00000
125 42 TIP3 H1 1.72889 6.24444 -2.17508 WAT0 42 0.00000
126 42 TIP3 H2 0.69206 6.68697 -3.18554 WAT0 42 0.00000
127 43 TIP3 OH2 -4.21073 5.91962 6.92364 WAT0 43 0.00000
128 43 TIP3 H1 -4.20320 5.78359 5.97619 WAT0 43 0.00000
129 43 TIP3 H2 -5.12669 5.80243 7.17564 WAT0 43 0.00000
130 44 TIP3 OH2 7.22748 -9.03800 -6.57484 WAT0 44 0.00000
131 44 TIP3 H1 6.32755 -8.89910 -6.27978 WAT0 44 0.00000
132 44 TIP3 H2 7.47932 -8.20654 -6.97667 WAT0 44 0.00000
133 45 TIP3 OH2 -4.70667 -0.25028 -4.60115 WAT0 45 0.00000
134 45 TIP3 H1 -4.99854 0.51789 -5.09202 WAT0 45 0.00000
135 45 TIP3 H2 -5.38115 -0.90966 -4.76401 WAT0 45 0.00000
136 46 TIP3 OH2 8.41662 5.32824 -8.19845 WAT0 46 0.00000
137 46 TIP3 H1 8.48997 6.26726 -8.02792 WAT0 46 0.00000
138 46 TIP3 H2 9.32213 5.02310 -8.25472 WAT0 46 0.00000
139 47 TIP3 OH2 -8.61366 2.11264 4.21383 WAT0 47 0.00000
140 47 TIP3 H1 -9.11482 2.08458 3.39880 WAT0 47 0.00000
141 47 TIP3 H2 -8.60829 1.20696 4.52356 WAT0 47 0.00000
142 48 TIP3 OH2 -8.86339 4.89302 1.09785 WAT0 48 0.00000
143 48 TIP3 H1 -7.91733 4.74872 1.07880 WAT0 48 0.00000
144 48 TIP3 H2 -8.97576 5.67730 1.63497 WAT0 48 0.00000
145 49 TIP3 OH2 9.33446 5.55899 6.78022 WAT0 49 0.00000
146 49 TIP3 H1 9.28514 4.60380 6.74298 WAT0 49 0.00000
147 49 TIP3 H2 8.50769 5.82652 7.18160 WAT0 49 0.00000
148 50 TIP3 OH2 0.31286 5.13291 5.65636 WAT0 50 0.00000
149 50 TIP3 H1 0.40032 5.95937 6.13127 WAT0 50 0.00000
150 50 TIP3 H2 -0.55063 4.80329 5.90529 WAT0 50 0.00000
151 51 TIP3 OH2 0.72744 8.90528 -4.53758 WAT0 51 0.00000
152 51 TIP3 H1 0.65204 8.78400 -5.48406 WAT0 51 0.00000
153 51 TIP3 H2 0.76031 9.85455 -4.41912 WAT0 51 0.00000
154 52 TIP3 OH2 -5.61918 7.69398 -2.75668 WAT0 52 0.00000
155 52 TIP3 H1 -5.46714 7.34602 -1.87803 WAT0 52 0.00000
156 52 TIP3 H2 -6.47014 7.33771 -3.01196 WAT0 52 0.00000
157 53 TIP3 OH2 3.82904 8.05930 -7.53534 WAT0 53 0.00000
158 53 TIP3 H1 4.20388 7.31491 -8.00608 WAT0 53 0.00000
159 53 TIP3 H2 3.83341 7.78936 -6.61701 WAT0 53 0.00000
160 54 TIP3 OH2 3.49785 7.98501 -4.78612 WAT0 54 0.00000
161 54 TIP3 H1 2.56283 8.08520 -4.60742 WAT0 54 0.00000
162 54 TIP3 H2 3.77804 7.27561 -4.20780 WAT0 54 0.00000
163 55 TIP3 OH2 6.48644 -2.94776 7.26044 WAT0 55 0.00000
164 55 TIP3 H1 6.07912 -2.46720 6.53977 WAT0 55 0.00000
165 55 TIP3 H2 6.52701 -3.85316 6.95252 WAT0 55 0.00000
166 56 TIP3 OH2 -6.36461 3.43618 5.25711 WAT0 56 0.00000
167 56 TIP3 H1 -6.14848 3.07474 6.11669 WAT0 56 0.00000
168 56 TIP3 H2 -7.22014 3.06156 5.04746 WAT0 56 0.00000
169 57 TIP3 OH2 -3.74581 -8.09377 1.25253 WAT0 57 0.00000
170 57 TIP3 H1 -4.60744 -8.18095 0.84482 WAT0 57 0.00000
171 57 TIP3 H2 -3.76824 -7.23776 1.68029 WAT0 57 0.00000
172 58 TIP3 OH2 0.91697 -8.37173 4.62723 WAT0 58 0.00000
173 58 TIP3 H1 1.33728 -8.78702 5.38029 WAT0 58 0.00000
174 58 TIP3 H2 -0.01607 -8.55040 4.74443 WAT0 58 0.00000
175 59 TIP3 OH2 4.24346 -4.61621 5.48068 WAT0 59 0.00000
176 59 TIP3 H1 3.72941 -4.74199 6.27828 WAT0 59 0.00000
177 59 TIP3 H2 4.08793 -3.70390 5.23630 WAT0 59 0.00000
178 60 TIP3 OH2 5.00595 0.24479 -8.75802 WAT0 60 0.00000
179 60 TIP3 H1 5.04803 0.02218 -9.68802 WAT0 60 0.00000
180 60 TIP3 H2 5.85516 0.64350 -8.56803 WAT0 60 0.00000
181 61 TIP3 OH2 0.57870 -5.87939 -8.08769 WAT0 61 0.00000
182 61 TIP3 H1 0.32518 -5.86023 -7.16488 WAT0 61 0.00000
183 61 TIP3 H2 0.32191 -6.75085 -8.38907 WAT0 61 0.00000
184 62 TIP3 OH2 -3.65480 -3.12832 2.34755 WAT0 62 0.00000
185 62 TIP3 H1 -4.29659 -3.16859 3.05656 WAT0 62 0.00000
186 62 TIP3 H2 -3.61760 -2.20185 2.10985 WAT0 62 0.00000
187 63 TIP3 OH2 -3.65789 -2.90731 -2.74045 WAT0 63 0.00000
188 63 TIP3 H1 -4.55060 -3.24770 -2.79907 WAT0 63 0.00000
189 63 TIP3 H2 -3.20723 -3.28422 -3.49613 WAT0 63 0.00000
190 64 TIP3 OH2 1.87766 -2.49128 -3.92337 WAT0 64 0.00000
191 64 TIP3 H1 1.46869 -1.67642 -4.21489 WAT0 64 0.00000
192 64 TIP3 H2 2.59828 -2.63127 -4.53766 WAT0 64 0.00000
193 65 TIP3 OH2 0.97982 -2.31564 7.56470 WAT0 65 0.00000
194 65 TIP3 H1 0.41720 -3.02048 7.88548 WAT0 65 0.00000
195 65 TIP3 H2 1.80616 -2.43645 8.03246 WAT0 65 0.00000
196 66 TIP3 OH2 2.88243 -3.04524 -1.10940 WAT0 66 0.00000
197 66 TIP3 H1 2.68688 -2.43956 -1.82434 WAT0 66 0.00000
198 66 TIP3 H2 3.06369 -3.87872 -1.54377 WAT0 66 0.00000
199 67 TIP3 OH2 -5.90475 -2.80797 4.21475 WAT0 67 0.00000
200 67 TIP3 H1 -5.94281 -2.40781 5.08346 WAT0 67 0.00000
201 67 TIP3 H2 -6.39564 -3.62473 4.30504 WAT0 67 0.00000
202 68 TIP3 OH2 -2.53901 -5.43374 -8.98665 WAT0 68 0.00000
203 68 TIP3 H1 -2.96994 -5.87873 -8.25691 WAT0 68 0.00000
204 68 TIP3 H2 -3.25714 -5.06211 -9.49890 WAT0 68 0.00000
205 69 TIP3 OH2 -9.29667 -5.69179 -1.93478 WAT0 69 0.00000
206 69 TIP3 H1 -8.66590 -5.72058 -1.21539 WAT0 69 0.00000
207 69 TIP3 H2 -8.84724 -6.11692 -2.66519 WAT0 69 0.00000
208 70 TIP3 OH2 -8.02246 -4.94559 -6.51074 WAT0 70 0.00000
209 70 TIP3 H1 -7.54829 -4.35460 -7.09565 WAT0 70 0.00000
210 70 TIP3 H2 -8.73982 -4.41530 -6.16373 WAT0 70 0.00000
211 71 TIP3 OH2 2.14635 -1.40711 3.56184 WAT0 71 0.00000
212 71 TIP3 H1 2.46983 -2.03814 2.91889 WAT0 71 0.00000
213 71 TIP3 H2 1.70628 -1.94189 4.22258 WAT0 71 0.00000
214 72 TIP3 OH2 -1.07636 -5.47956 -1.65404 WAT0 72 0.00000
215 72 TIP3 H1 -1.98725 -5.42288 -1.36544 WAT0 72 0.00000
216 72 TIP3 H2 -0.57107 -5.54001 -0.84332 WAT0 72 0.00000
217 73 TIP3 OH2 -6.24802 -3.85093 -2.82728 WAT0 73 0.00000
218 73 TIP3 H1 -7.13722 -3.75138 -3.16732 WAT0 73 0.00000
219 73 TIP3 H2 -5.95153 -4.69263 -3.17349 WAT0 73 0.00000
220 74 TIP3 OH2 -2.59484 -3.85067 -5.17082 WAT0 74 0.00000
221 74 TIP3 H1 -1.66329 -3.72167 -4.99251 WAT0 74 0.00000
222 74 TIP3 H2 -2.80981 -3.18124 -5.82035 WAT0 74 0.00000
223 75 TIP3 OH2 3.32883 -6.24493 1.61014 WAT0 75 0.00000
224 75 TIP3 H1 2.65199 -6.11362 2.27411 WAT0 75 0.00000
225 75 TIP3 H2 2.84332 -6.39998 0.79991 WAT0 75 0.00000
226 76 TIP3 OH2 -3.92082 -2.65645 -7.60421 WAT0 76 0.00000
227 76 TIP3 H1 -4.46331 -3.03607 -8.29545 WAT0 76 0.00000
228 76 TIP3 H2 -3.08733 -2.46198 -8.03280 WAT0 76 0.00000
229 77 TIP3 OH2 6.61634 9.42661 7.88690 WAT0 77 0.00000
230 77 TIP3 H1 6.81621 9.85080 7.05243 WAT0 77 0.00000
231 77 TIP3 H2 7.27171 9.77043 8.49394 WAT0 77 0.00000
232 78 TIP3 OH2 -5.78568 1.90074 7.49495 WAT0 78 0.00000
233 78 TIP3 H1 -5.05344 2.15533 8.05640 WAT0 78 0.00000
234 78 TIP3 H2 -6.56581 2.10528 8.01049 WAT0 78 0.00000
235 79 TIP3 OH2 0.24361 -2.69226 0.23292 WAT0 79 0.00000
236 79 TIP3 H1 0.80795 -3.23860 -0.31412 WAT0 79 0.00000
237 79 TIP3 H2 0.09595 -3.21407 1.02168 WAT0 79 0.00000
238 80 TIP3 OH2 -4.75442 -6.55565 -3.34860 WAT0 80 0.00000
239 80 TIP3 H1 -5.07147 -7.45812 -3.38406 WAT0 80 0.00000
240 80 TIP3 H2 -3.97301 -6.55391 -3.90144 WAT0 80 0.00000
241 81 TIP3 OH2 -1.12980 -4.30365 2.64696 WAT0 81 0.00000
242 81 TIP3 H1 -1.96527 -3.84970 2.75720 WAT0 81 0.00000
243 81 TIP3 H2 -0.60574 -4.02780 3.39895 WAT0 81 0.00000
244 82 TIP3 OH2 -0.58554 1.90912 -5.66840 WAT0 82 0.00000
245 82 TIP3 H1 -1.33044 1.40165 -5.99061 WAT0 82 0.00000
246 82 TIP3 H2 -0.71982 1.95792 -4.72192 WAT0 82 0.00000
247 83 TIP3 OH2 6.56435 1.04194 3.11836 WAT0 83 0.00000
248 83 TIP3 H1 7.20623 1.49857 2.57458 WAT0 83 0.00000
249 83 TIP3 H2 5.73404 1.15518 2.65577 WAT0 83 0.00000
250 84 TIP3 OH2 3.31214 -5.27689 -7.46914 WAT0 84 0.00000
251 84 TIP3 H1 2.37356 -5.16533 -7.62026 WAT0 84 0.00000
252 84 TIP3 H2 3.60935 -4.42020 -7.16257 WAT0 84 0.00000
253 85 TIP3 OH2 0.93367 2.09345 5.56851 WAT0 85 0.00000
254 85 TIP3 H1 0.58828 1.71169 6.37547 WAT0 85 0.00000
255 85 TIP3 H2 0.73368 3.02681 5.63980 WAT0 85 0.00000
256 86 TIP3 OH2 4.03049 -3.40962 -5.80840 WAT0 86 0.00000
257 86 TIP3 H1 4.92239 -3.54712 -5.48928 WAT0 86 0.00000
258 86 TIP3 H2 4.08685 -2.61901 -6.34505 WAT0 86 0.00000
259 87 TIP3 OH2 -5.46071 1.20412 0.10139 WAT0 87 0.00000
260 87 TIP3 H1 -4.71599 1.20169 -0.49996 WAT0 87 0.00000
261 87 TIP3 H2 -5.38305 0.38050 0.58290 WAT0 87 0.00000
262 88 TIP3 OH2 1.53987 3.36755 -6.64294 WAT0 88 0.00000
263 88 TIP3 H1 1.24471 4.19434 -6.26146 WAT0 88 0.00000
264 88 TIP3 H2 0.83687 2.74824 -6.44680 WAT0 88 0.00000
265 89 TIP3 OH2 -8.45274 -0.33519 5.41624 WAT0 89 0.00000
266 89 TIP3 H1 -8.22988 -0.75323 6.24799 WAT0 89 0.00000
267 89 TIP3 H2 -9.05473 -0.94769 4.99352 WAT0 89 0.00000
268 90 TIP3 OH2 -1.43625 -0.81820 7.62921 WAT0 90 0.00000
269 90 TIP3 H1 -1.73217 -0.98390 6.73412 WAT0 90 0.00000
270 90 TIP3 H2 -0.50473 -1.03817 7.61860 WAT0 90 0.00000
271 91 TIP3 OH2 3.18403 4.55500 5.51901 WAT0 91 0.00000
272 91 TIP3 H1 2.28346 4.73826 5.25140 WAT0 91 0.00000
273 91 TIP3 H2 3.21814 4.81393 6.43989 WAT0 91 0.00000
274 92 TIP3 OH2 8.91536 -3.20021 -6.11373 WAT0 92 0.00000
275 92 TIP3 H1 8.36099 -3.59641 -6.78598 WAT0 92 0.00000
276 92 TIP3 H2 9.01572 -2.28969 -6.39140 WAT0 92 0.00000
277 93 TIP3 OH2 8.87856 2.59996 6.72342 WAT0 93 0.00000
278 93 TIP3 H1 8.02741 2.83834 6.35606 WAT0 93 0.00000
279 93 TIP3 H2 9.46890 2.58328 5.97013 WAT0 93 0.00000
280 94 TIP3 OH2 7.21053 5.58583 -5.64852 WAT0 94 0.00000
281 94 TIP3 H1 6.83764 4.76021 -5.33946 WAT0 94 0.00000
282 94 TIP3 H2 7.48788 5.40277 -6.54618 WAT0 94 0.00000
283 95 TIP3 OH2 4.37092 0.39378 1.37267 WAT0 95 0.00000
284 95 TIP3 H1 3.44261 0.16197 1.34560 WAT0 95 0.00000
285 95 TIP3 H2 4.82203 -0.38324 1.04255 WAT0 95 0.00000
286 96 TIP3 OH2 -3.08577 4.72194 -2.49446 WAT0 96 0.00000
287 96 TIP3 H1 -2.55855 5.49538 -2.69458 WAT0 96 0.00000
288 96 TIP3 H2 -3.96592 4.94686 -2.79606 WAT0 96 0.00000
289 97 TIP3 OH2 -7.33100 -0.41565 -7.90722 WAT0 97 0.00000
290 97 TIP3 H1 -6.71501 0.21107 -7.52774 WAT0 97 0.00000
291 97 TIP3 H2 -8.19274 -0.09967 -7.63557 WAT0 97 0.00000
292 98 TIP3 OH2 -1.65854 2.38493 -2.91803 WAT0 98 0.00000
293 98 TIP3 H1 -1.89954 3.31037 -2.87650 WAT0 98 0.00000
294 98 TIP3 H2 -2.39918 1.92606 -2.52164 WAT0 98 0.00000
295 99 TIP3 OH2 -1.14388 6.53429 3.39708 WAT0 99 0.00000
296 99 TIP3 H1 -0.78141 7.38885 3.16352 WAT0 99 0.00000
297 99 TIP3 H2 -0.61236 6.24245 4.13771 WAT0 99 0.00000
298 100 TIP3 OH2 -2.97546 7.40669 -3.37281 WAT0 100 0.00000
299 100 TIP3 H1 -3.92541 7.51243 -3.32148 WAT0 100 0.00000
300 100 TIP3 H2 -2.62365 8.22743 -3.02806 WAT0 100 0.00000
301 101 TIP3 OH2 2.40020 2.63336 3.09764 WAT0 101 0.00000
302 101 TIP3 H1 1.97433 2.40553 3.92404 WAT0 101 0.00000
303 101 TIP3 H2 2.98078 1.89454 2.91517 WAT0 101 0.00000
304 102 TIP3 OH2 4.60309 3.56241 -7.82846 WAT0 102 0.00000
305 102 TIP3 H1 4.95640 3.18239 -7.02411 WAT0 102 0.00000
306 102 TIP3 H2 3.65444 3.46889 -7.74153 WAT0 102 0.00000
307 103 TIP3 OH2 5.05862 7.18531 5.56712 WAT0 103 0.00000
308 103 TIP3 H1 4.45694 6.62960 5.07175 WAT0 103 0.00000
309 103 TIP3 H2 5.33999 7.85229 4.94086 WAT0 103 0.00000
310 104 TIP3 OH2 9.10653 8.04166 -7.62744 WAT0 104 0.00000
311 104 TIP3 H1 9.85032 8.62771 -7.76728 WAT0 104 0.00000
312 104 TIP3 H2 8.41234 8.61024 -7.29420 WAT0 104 0.00000
313 105 TIP3 OH2 -6.81879 -5.58192 4.97438 WAT0 105 0.00000
314 105 TIP3 H1 -7.71156 -5.24338 4.90678 WAT0 105 0.00000
315 105 TIP3 H2 -6.91751 -6.43731 5.39246 WAT0 105 0.00000
316 106 TIP3 OH2 5.46902 2.23461 -5.60167 WAT0 106 0.00000
317 106 TIP3 H1 5.19178 1.50654 -5.04556 WAT0 106 0.00000
318 106 TIP3 H2 6.39632 2.35381 -5.39641 WAT0 106 0.00000
319 107 TIP3 OH2 -7.16759 6.22252 3.40932 WAT0 107 0.00000
320 107 TIP3 H1 -6.95056 5.29076 3.37829 WAT0 107 0.00000
321 107 TIP3 H2 -6.92124 6.49702 4.29260 WAT0 107 0.00000
322 108 TIP3 OH2 -1.30613 4.67402 -9.38146 WAT0 108 0.00000
323 108 TIP3 H1 -1.06715 3.92583 -9.92857 WAT0 108 0.00000
324 108 TIP3 H2 -1.57500 4.28619 -8.54868 WAT0 108 0.00000
325 109 TIP3 OH2 -2.36907 4.24440 -6.92520 WAT0 109 0.00000
326 109 TIP3 H1 -2.22227 3.72438 -6.13511 WAT0 109 0.00000
327 109 TIP3 H2 -2.37190 5.15116 -6.61861 WAT0 109 0.00000
328 110 TIP3 OH2 -5.91596 1.49673 -6.41466 WAT0 110 0.00000
329 110 TIP3 H1 -6.60203 1.84898 -5.84769 WAT0 110 0.00000
330 110 TIP3 H2 -5.39317 2.25969 -6.66123 WAT0 110 0.00000
331 111 TIP3 OH2 1.91555 -5.84089 3.86424 WAT0 111 0.00000
332 111 TIP3 H1 2.61434 -5.76702 4.51421 WAT0 111 0.00000
333 111 TIP3 H2 1.53469 -6.70539 4.01853 WAT0 111 0.00000
334 112 TIP3 OH2 2.70004 -6.18872 -5.03853 WAT0 112 0.00000
335 112 TIP3 H1 2.91987 -5.71718 -5.84199 WAT0 112 0.00000
336 112 TIP3 H2 3.25844 -5.79446 -4.36847 WAT0 112 0.00000
337 113 TIP3 OH2 0.36865 5.94176 -6.17578 WAT0 113 0.00000
338 113 TIP3 H1 -0.44774 6.43873 -6.12335 WAT0 113 0.00000
339 113 TIP3 H2 0.89828 6.41711 -6.81590 WAT0 113 0.00000
340 114 TIP3 OH2 -0.09997 -4.46084 -4.20369 WAT0 114 0.00000
341 114 TIP3 H1 0.71229 -3.95652 -4.15752 WAT0 114 0.00000
342 114 TIP3 H2 -0.34467 -4.60587 -3.28973 WAT0 114 0.00000
343 115 TIP3 OH2 0.43567 -3.47457 4.98097 WAT0 115 0.00000
344 115 TIP3 H1 0.55470 -2.90103 5.73801 WAT0 115 0.00000
345 115 TIP3 H2 1.09113 -4.16263 5.09575 WAT0 115 0.00000
346 116 TIP3 OH2 0.78370 -7.37954 -3.26558 WAT0 116 0.00000
347 116 TIP3 H1 0.43705 -6.76248 -2.62115 WAT0 116 0.00000
348 116 TIP3 H2 1.44239 -6.87897 -3.74703 WAT0 116 0.00000
349 117 TIP3 OH2 -2.29304 6.98548 -6.19409 WAT0 117 0.00000
350 117 TIP3 H1 -2.13217 7.78523 -6.69483 WAT0 117 0.00000
351 117 TIP3 H2 -2.49026 7.29208 -5.30903 WAT0 117 0.00000
352 118 TIP3 OH2 -3.55860 -6.31660 -6.57833 WAT0 118 0.00000
353 118 TIP3 H1 -3.64212 -5.42829 -6.23169 WAT0 118 0.00000
354 118 TIP3 H2 -2.66857 -6.58193 -6.34665 WAT0 118 0.00000
355 119 TIP3 OH2 6.64025 -5.56754 5.81594 WAT0 119 0.00000
356 119 TIP3 H1 5.72383 -5.30537 5.72831 WAT0 119 0.00000
357 119 TIP3 H2 6.97575 -5.57064 4.91947 WAT0 119 0.00000
358 120 TIP3 OH2 5.24235 -1.81744 -0.08833 WAT0 120 0.00000
359 120 TIP3 H1 4.44479 -2.23242 -0.41683 WAT0 120 0.00000
360 120 TIP3 H2 5.68746 -2.50807 0.40272 WAT0 120 0.00000
361 121 TIP3 OH2 -5.30007 4.11062 -7.51788 WAT0 121 0.00000
362 121 TIP3 H1 -4.70792 4.81010 -7.24164 WAT0 121 0.00000
363 121 TIP3 H2 -4.84077 3.67757 -8.23742 WAT0 121 0.00000
364 122 TIP3 OH2 -6.98415 -3.22508 -8.40194 WAT0 122 0.00000
365 122 TIP3 H1 -7.02889 -2.28577 -8.22324 WAT0 122 0.00000
366 122 TIP3 H2 -7.87183 -3.46059 -8.67173 WAT0 122 0.00000
367 123 TIP3 OH2 6.32881 7.43881 1.53402 WAT0 123 0.00000
368 123 TIP3 H1 6.17324 8.11725 0.87695 WAT0 123 0.00000
369 123 TIP3 H2 7.26145 7.51074 1.73708 WAT0 123 0.00000
370 124 TIP3 OH2 -6.17595 -8.44342 0.27116 WAT0 124 0.00000
371 124 TIP3 H1 -6.40497 -8.38417 -0.65634 WAT0 124 0.00000
372 124 TIP3 H2 -6.61861 -9.23487 0.57757 WAT0 124 0.00000
373 125 TIP3 OH2 -7.24562 5.49729 -3.56826 WAT0 125 0.00000
374 125 TIP3 H1 -8.07776 5.96956 -3.54112 WAT0 125 0.00000
375 125 TIP3 H2 -6.69979 6.00705 -4.16695 WAT0 125 0.00000
376 126 TIP3 OH2 -7.95725 8.10966 7.76154 WAT0 126 0.00000
377 126 TIP3 H1 -7.41703 7.89306 8.52146 WAT0 126 0.00000
378 126 TIP3 H2 -8.43845 7.30426 7.57179 WAT0 126 0.00000
379 127 TIP3 OH2 -3.35991 7.02910 9.38196 WAT0 127 0.00000
380 127 TIP3 H1 -2.59219 6.57018 9.72288 WAT0 127 0.00000
381 127 TIP3 H2 -3.38129 6.80308 8.45208 WAT0 127 0.00000
382 128 TIP3 OH2 0.73205 6.53716 -9.24286 WAT0 128 0.00000
383 128 TIP3 H1 0.08815 5.90602 -8.92149 WAT0 128 0.00000
384 128 TIP3 H2 1.49388 6.00596 -9.47451 WAT0 128 0.00000
385 129 TIP3 OH2 3.21696 5.40921 8.11111 WAT0 129 0.00000
386 129 TIP3 H1 2.86591 4.55251 8.35415 WAT0 129 0.00000
387 129 TIP3 H2 3.94328 5.55188 8.71801 WAT0 129 0.00000
388 130 TIP3 OH2 5.33634 6.35415 -9.00906 WAT0 130 0.00000
389 130 TIP3 H1 5.61938 5.55967 -8.55637 WAT0 130 0.00000
390 130 TIP3 H2 6.07613 6.58725 -9.56995 WAT0 130 0.00000
391 131 TIP3 OH2 -8.05030 1.92007 8.71597 WAT0 131 0.00000
392 131 TIP3 H1 -7.90625 1.01814 8.42964 WAT0 131 0.00000
393 131 TIP3 H2 -8.82256 2.20628 8.22820 WAT0 131 0.00000
394 132 TIP3 OH2 -3.70893 2.26364 -9.15157 WAT0 132 0.00000
395 132 TIP3 H1 -3.64452 1.46960 -8.62093 WAT0 132 0.00000
396 132 TIP3 H2 -3.05601 2.14492 -9.84137 WAT0 132 0.00000
397 133 TIP3 OH2 -1.39469 1.88988 8.14861 WAT0 133 0.00000
398 133 TIP3 H1 -1.72331 2.16069 7.29135 WAT0 133 0.00000
399 133 TIP3 H2 -1.24287 0.94886 8.06111 WAT0 133 0.00000
400 134 TIP3 OH2 1.64341 3.31081 -9.41577 WAT0 134 0.00000
401 134 TIP3 H1 1.37482 3.49102 -8.51488 WAT0 134 0.00000
402 134 TIP3 H2 1.43697 2.38543 -9.54719 WAT0 134 0.00000
403 135 TIP3 OH2 4.33983 1.80561 5.53184 WAT0 135 0.00000
404 135 TIP3 H1 5.08531 2.39398 5.41224 WAT0 135 0.00000
405 135 TIP3 H2 3.58251 2.38758 5.59515 WAT0 135 0.00000
406 136 TIP3 OH2 -7.21765 -0.87960 8.13590 WAT0 136 0.00000
407 136 TIP3 H1 -6.80953 -1.73694 8.01496 WAT0 136 0.00000
408 136 TIP3 H2 -7.47789 -0.86547 9.05693 WAT0 136 0.00000
409 137 TIP3 OH2 -2.55955 0.23626 -6.84577 WAT0 137 0.00000
410 137 TIP3 H1 -3.01935 -0.24791 -6.15992 WAT0 137 0.00000
411 137 TIP3 H2 -2.30468 -0.43220 -7.48172 WAT0 137 0.00000
412 138 TIP3 OH2 -3.27062 -1.87103 5.51019 WAT0 138 0.00000
413 138 TIP3 H1 -3.88901 -1.19637 5.79066 WAT0 138 0.00000
414 138 TIP3 H2 -2.92650 -1.54964 4.67681 WAT0 138 0.00000
415 139 TIP3 OH2 -1.48851 -1.52056 -8.58345 WAT0 139 0.00000
416 139 TIP3 H1 -1.66901 -1.67544 -9.51062 WAT0 139 0.00000
417 139 TIP3 H2 -0.53846 -1.41269 -8.53866 WAT0 139 0.00000
418 140 TIP3 OH2 1.74920 0.60050 8.78767 WAT0 140 0.00000
419 140 TIP3 H1 2.70232 0.68441 8.76027 WAT0 140 0.00000
420 140 TIP3 H2 1.58866 -0.11132 9.40716 WAT0 140 0.00000
421 141 TIP3 OH2 7.90132 0.83386 -9.13764 WAT0 141 0.00000
422 141 TIP3 H1 7.62780 0.40941 -9.95081 WAT0 141 0.00000
423 141 TIP3 H2 7.94073 1.76531 -9.35460 WAT0 141 0.00000
424 142 TIP3 OH2 -2.93125 -4.51595 6.59250 WAT0 142 0.00000
425 142 TIP3 H1 -2.78116 -5.24482 5.99047 WAT0 142 0.00000
426 142 TIP3 H2 -2.92901 -3.73878 6.03372 WAT0 142 0.00000
427 143 TIP3 OH2 -2.51868 -6.14637 4.08524 WAT0 143 0.00000
428 143 TIP3 H1 -1.98293 -5.69470 3.43317 WAT0 143 0.00000
429 143 TIP3 H2 -3.37072 -6.25439 3.66265 WAT0 143 0.00000
430 144 TIP3 OH2 -0.93684 -0.70675 4.32476 WAT0 144 0.00000
431 144 TIP3 H1 -0.18636 -0.86300 3.75154 WAT0 144 0.00000
432 144 TIP3 H2 -1.27601 0.14491 4.04931 WAT0 144 0.00000
433 145 TIP3 OH2 3.47878 -2.89157 9.35329 WAT0 145 0.00000
434 145 TIP3 H1 3.67091 -3.82263 9.24174 WAT0 145 0.00000
435 145 TIP3 H2 4.33641 -2.46662 9.34283 WAT0 145 0.00000
436 146 TIP3 OH2 4.79550 -0.10305 7.43056 WAT0 146 0.00000
437 146 TIP3 H1 4.51400 0.60641 6.85294 WAT0 146 0.00000
438 146 TIP3 H2 5.73793 -0.17575 7.27968 WAT0 146 0.00000
439 147 TIP3 OH2 -4.45262 -3.31760 8.50406 WAT0 147 0.00000
440 147 TIP3 H1 -5.21972 -3.85012 8.29382 WAT0 147 0.00000
441 147 TIP3 H2 -3.77372 -3.62756 7.90469 WAT0 147 0.00000
442 148 TIP3 OH2 -1.71313 -8.68980 4.51660 WAT0 148 0.00000
443 148 TIP3 H1 -1.81117 -7.74348 4.41122 WAT0 148 0.00000
444 148 TIP3 H2 -2.45551 -9.06242 4.04095 WAT0 148 0.00000
445 149 TIP3 OH2 -0.44908 -4.36826 8.08044 WAT0 149 0.00000
446 149 TIP3 H1 -0.68454 -4.58759 8.98193 WAT0 149 0.00000
447 149 TIP3 H2 -1.23239 -4.57514 7.57069 WAT0 149 0.00000
448 150 TIP3 OH2 2.26658 -5.24091 7.15579 WAT0 150 0.00000
449 150 TIP3 H1 1.31912 -5.20894 7.28812 WAT0 150 0.00000
450 150 TIP3 H2 2.57925 -5.86620 7.80961 WAT0 150 0.00000
451 151 TIP3 OH2 3.90073 -6.60680 9.16098 WAT0 151 0.00000
452 151 TIP3 H1 3.80391 -7.55907 9.15517 WAT0 151 0.00000
453 151 TIP3 H2 3.57904 -6.33812 10.02153 WAT0 151 0.00000
454 152 TIP3 OH2 -6.27234 -5.39722 8.20853 WAT0 152 0.00000
455 152 TIP3 H1 -6.06060 -6.10361 7.59828 WAT0 152 0.00000
456 152 TIP3 H2 -6.38359 -5.83462 9.05265 WAT0 152 0.00000
457 153 TIP3 OH2 -1.49132 -9.39606 7.18788 WAT0 153 0.00000
458 153 TIP3 H1 -0.77948 -10.03584 7.17379 WAT0 153 0.00000
459 153 TIP3 H2 -1.59228 -9.12923 6.27419 WAT0 153 0.00000
460 154 TIP3 OH2 -1.13757 -7.71322 9.24151 WAT0 154 0.00000
461 154 TIP3 H1 -1.26935 -8.18884 8.42136 WAT0 154 0.00000
462 154 TIP3 H2 -1.73683 -6.96886 9.18622 WAT0 154 0.00000
463 155 TIP3 OH2 -1.59134 9.16981 -7.58209 WAT0 155 0.00000
464 155 TIP3 H1 -0.65827 9.32768 -7.43825 WAT0 155 0.00000
465 155 TIP3 H2 -1.85546 9.84511 -8.20694 WAT0 155 0.00000
466 156 TIP3 OH2 -8.02285 3.80619 -8.09928 WAT0 156 0.00000
467 156 TIP3 H1 -7.10893 3.88508 -7.82589 WAT0 156 0.00000
468 156 TIP3 H2 -8.01554 3.11915 -8.76572 WAT0 156 0.00000
469 157 TIP3 OH2 -9.37379 9.19904 -3.02189 WAT0 157 0.00000
470 157 TIP3 H1 -10.02108 8.73721 -3.55477 WAT0 157 0.00000
471 157 TIP3 H2 -9.01933 8.52737 -2.43927 WAT0 157 0.00000
472 158 TIP3 OH2 -8.50387 7.27974 -1.21727 WAT0 158 0.00000
473 158 TIP3 H1 -8.83819 6.39947 -1.04525 WAT0 158 0.00000
474 158 TIP3 H2 -8.28163 7.62524 -0.35271 WAT0 158 0.00000
475 159 TIP3 OH2 9.04461 8.08938 1.76321 WAT0 159 0.00000
476 159 TIP3 H1 9.02328 8.27422 2.70215 WAT0 159 0.00000
477 159 TIP3 H2 9.73523 8.65778 1.42235 WAT0 159 0.00000
478 160 TIP3 OH2 8.60790 7.65649 4.68512 WAT0 160 0.00000
479 160 TIP3 H1 8.12077 6.92090 4.31386 WAT0 160 0.00000
480 160 TIP3 H2 9.15717 7.26288 5.36306 WAT0 160 0.00000
481 161 TIP3 OH2 7.05863 3.44630 9.32315 WAT0 161 0.00000
482 161 TIP3 H1 6.19274 3.34127 9.71738 WAT0 161 0.00000
483 161 TIP3 H2 7.43522 4.20463 9.76962 WAT0 161 0.00000
484 162 TIP3 OH2 8.35960 1.70267 -5.16260 WAT0 162 0.00000
485 162 TIP3 H1 9.20974 2.12376 -5.03544 WAT0 162 0.00000
486 162 TIP3 H2 8.36511 0.96268 -4.55546 WAT0 162 0.00000
487 163 TIP3 OH2 8.75416 -0.24359 -3.33903 WAT0 163 0.00000
488 163 TIP3 H1 8.02762 -0.72333 -2.94127 WAT0 163 0.00000
489 163 TIP3 H2 9.33549 -0.03812 -2.60687 WAT0 163 0.00000
490 164 TIP3 OH2 8.51328 2.54116 1.60873 WAT0 164 0.00000
491 164 TIP3 H1 9.34670 2.16316 1.32809 WAT0 164 0.00000
492 164 TIP3 H2 8.62531 3.48428 1.48964 WAT0 164 0.00000
493 165 TIP3 OH2 6.99951 5.41891 3.91557 WAT0 165 0.00000
494 165 TIP3 H1 6.35204 5.74406 4.54109 WAT0 165 0.00000
495 165 TIP3 H2 6.48191 4.97868 3.24140 WAT0 165 0.00000
496 166 TIP3 OH2 9.02247 -0.34274 -6.94790 WAT0 166 0.00000
497 166 TIP3 H1 8.50058 0.01367 -7.66681 WAT0 166 0.00000
498 166 TIP3 H2 8.98939 0.33204 -6.26981 WAT0 166 0.00000
499 167 TIP3 OH2 7.37137 -3.10318 -8.39719 WAT0 167 0.00000
500 167 TIP3 H1 7.46781 -2.43648 -9.07722 WAT0 167 0.00000
501 167 TIP3 H2 7.23133 -3.91855 -8.87864 WAT0 167 0.00000
502 168 TIP3 OH2 6.54084 -1.72294 -2.77616 WAT0 168 0.00000
503 168 TIP3 H1 6.39072 -2.66808 -2.79638 WAT0 168 0.00000
504 168 TIP3 H2 6.18729 -1.44180 -1.93225 WAT0 168 0.00000
505 169 TIP3 OH2 -8.42392 0.35528 1.23422 WAT0 169 0.00000
506 169 TIP3 H1 -8.23963 0.27345 0.29851 WAT0 169 0.00000
507 169 TIP3 H2 -7.57463 0.23098 1.65786 WAT0 169 0.00000
508 170 TIP3 OH2 7.39713 0.24739 6.86267 WAT0 170 0.00000
509 170 TIP3 H1 7.97986 -0.48738 7.05439 WAT0 170 0.00000
510 170 TIP3 H2 7.96106 1.01942 6.90925 WAT0 170 0.00000
511 171 TIP3 OH2 8.89384 -1.85003 7.54721 WAT0 171 0.00000
512 171 TIP3 H1 8.03051 -2.22882 7.38168 WAT0 171 0.00000
513 171 TIP3 H2 9.49821 -2.58855 7.47279 WAT0 171 0.00000
514 172 TIP3 OH2 6.61875 -5.69520 -9.27964 WAT0 172 0.00000
515 172 TIP3 H1 7.22933 -6.06652 -8.64282 WAT0 172 0.00000
516 172 TIP3 H2 5.78190 -6.11651 -9.08364 WAT0 172 0.00000
517 173 TIP3 OH2 6.25132 -4.14036 -4.31365 WAT0 173 0.00000
518 173 TIP3 H1 6.53103 -5.04732 -4.18948 WAT0 173 0.00000
519 173 TIP3 H2 7.01049 -3.70621 -4.70273 WAT0 173 0.00000
520 174 TIP3 OH2 6.86315 -3.55862 1.12224 WAT0 174 0.00000
521 174 TIP3 H1 7.79595 -3.34663 1.08784 WAT0 174 0.00000
522 174 TIP3 H2 6.62790 -3.45741 2.04454 WAT0 174 0.00000
523 175 TIP3 OH2 6.89234 -2.82209 3.89818 WAT0 175 0.00000
524 175 TIP3 H1 6.04947 -2.55405 4.26416 WAT0 175 0.00000
525 175 TIP3 H2 7.33477 -1.99990 3.68729 WAT0 175 0.00000
526 176 TIP3 OH2 -8.82644 -4.37422 7.37510 WAT0 176 0.00000
527 176 TIP3 H1 -7.90695 -4.49639 7.61141 WAT0 176 0.00000
528 176 TIP3 H2 -9.27599 -5.12425 7.76445 WAT0 176 0.00000
529 177 TIP3 OH2 9.17550 -8.84207 9.25168 WAT0 177 0.00000
530 177 TIP3 H1 9.52520 -9.49572 8.64615 WAT0 177 0.00000
531 177 TIP3 H2 9.32245 -8.00466 8.81194 WAT0 177 0.00000
532 178 TIP3 OH2 6.86480 -6.87743 -4.26545 WAT0 178 0.00000
533 178 TIP3 H1 7.04730 -7.32628 -3.43995 WAT0 178 0.00000
534 178 TIP3 H2 6.26509 -7.46199 -4.72899 WAT0 178 0.00000
535 179 TIP3 OH2 -7.60519 -6.06206 0.26639 WAT0 179 0.00000
536 179 TIP3 H1 -7.16003 -6.85381 0.56836 WAT0 179 0.00000
537 179 TIP3 H2 -7.13889 -5.34554 0.69695 WAT0 179 0.00000
538 180 TIP3 OH2 -9.30116 -3.06276 1.33541 WAT0 180 0.00000
539 180 TIP3 H1 -8.80918 -3.28371 0.54461 WAT0 180 0.00000
540 180 TIP3 H2 -8.93907 -2.22242 1.61636 WAT0 180 0.00000
541 181 TIP3 OH2 8.69522 -6.73261 7.60081 WAT0 181 0.00000
542 181 TIP3 H1 7.77779 -6.46190 7.56516 WAT0 181 0.00000
543 181 TIP3 H2 8.81816 -7.26777 6.81678 WAT0 181 0.00000
544 182 TIP3 OH2 8.73142 -6.80962 -7.73742 WAT0 182 0.00000
545 182 TIP3 H1 9.14368 -7.53105 -8.21262 WAT0 182 0.00000
546 182 TIP3 H2 9.41307 -6.14016 -7.67899 WAT0 182 0.00000
547 183 TIP3 OH2 -8.98751 -6.80485 -4.61035 WAT0 183 0.00000
548 183 TIP3 H1 -9.91267 -6.59619 -4.73980 WAT0 183 0.00000
549 183 TIP3 H2 -8.53352 -6.32077 -5.30012 WAT0 183 0.00000
550 184 TIP3 OH2 5.78321 8.17932 -2.66461 WAT0 184 0.00000
551 184 TIP3 H1 6.43550 7.83153 -3.27270 WAT0 184 0.00000
552 184 TIP3 H2 6.29359 8.66764 -2.01864 WAT0 184 0.00000
553 185 TIP3 OH2 -9.02397 -8.06695 3.73390 WAT0 185 0.00000
554 185 TIP3 H1 -9.68892 -8.31292 4.37699 WAT0 185 0.00000
555 185 TIP3 H2 -9.46684 -7.44491 3.15670 WAT0 185 0.00000
556 186 TIP3 OH2 -6.83204 5.10846 7.87848 WAT0 186 0.00000
557 186 TIP3 H1 -7.65279 5.28311 7.41795 WAT0 186 0.00000
558 186 TIP3 H2 -7.08426 5.03493 8.79892 WAT0 186 0.00000
559 187 TIP3 OH2 -3.87775 6.08258 4.13688 WAT0 187 0.00000
560 187 TIP3 H1 -4.30264 6.89243 3.85434 WAT0 187 0.00000
561 187 TIP3 H2 -2.97347 6.16799 3.83486 WAT0 187 0.00000
562 188 TIP3 OH2 0.43339 7.48158 7.09625 WAT0 188 0.00000
563 188 TIP3 H1 0.61814 7.14819 7.97428 WAT0 188 0.00000
564 188 TIP3 H2 1.27984 7.79144 6.77417 WAT0 188 0.00000
565 189 TIP3 OH2 2.77843 8.76747 6.34039 WAT0 189 0.00000
566 189 TIP3 H1 3.45532 8.13470 6.10031 WAT0 189 0.00000
567 189 TIP3 H2 3.10031 9.16852 7.14772 WAT0 189 0.00000
568 190 TIP3 OH2 7.69581 -8.64298 5.41989 WAT0 190 0.00000
569 190 TIP3 H1 6.88316 -8.31795 5.03236 WAT0 190 0.00000
570 190 TIP3 H2 7.92866 -9.40313 4.88680 WAT0 190 0.00000
571 191 TIP3 OH2 -6.47608 9.33897 4.18441 WAT0 191 0.00000
572 191 TIP3 H1 -7.19644 9.77907 3.73318 WAT0 191 0.00000
573 191 TIP3 H2 -6.84168 9.08844 5.03281 WAT0 191 0.00000
574 192 TIP3 OH2 -4.00882 8.93936 3.21413 WAT0 192 0.00000
575 192 TIP3 H1 -4.87360 9.01121 3.61814 WAT0 192 0.00000
576 192 TIP3 H2 -4.06392 9.48609 2.43038 WAT0 192 0.00000
577 193 TIP3 OH2 0.70174 8.82725 2.38973 WAT0 193 0.00000
578 193 TIP3 H1 0.24514 9.35622 1.73557 WAT0 193 0.00000
579 193 TIP3 H2 0.86454 9.43039 3.11496 WAT0 193 0.00000
580 194 TIP3 OH2 3.02937 7.70521 3.33476 WAT0 194 0.00000
581 194 TIP3 H1 2.12474 7.87023 3.06897 WAT0 194 0.00000
582 194 TIP3 H2 3.45823 8.55843 3.26910 WAT0 194 0.00000
583 195 TIP3 OH2 5.63356 9.27512 3.62954 WAT0 195 0.00000
584 195 TIP3 H1 5.45176 10.19101 3.41903 WAT0 195 0.00000
585 195 TIP3 H2 5.81034 8.86483 2.78300 WAT0 195 0.00000
586 196 TIP3 OH2 -7.06127 7.96222 1.09459 WAT0 196 0.00000
587 196 TIP3 H1 -7.07967 7.53673 1.95182 WAT0 196 0.00000
588 196 TIP3 H2 -6.25648 7.64372 0.68581 WAT0 196 0.00000
589 197 TIP3 OH2 -4.91996 6.67209 -0.25042 WAT0 197 0.00000
590 197 TIP3 H1 -5.13889 5.75583 -0.08082 WAT0 197 0.00000
591 197 TIP3 H2 -4.09574 6.81213 0.21572 WAT0 197 0.00000
592 198 TIP3 OH2 -2.38271 7.14202 0.59838 WAT0 198 0.00000
593 198 TIP3 H1 -2.17014 6.25392 0.31147 WAT0 198 0.00000
594 198 TIP3 H2 -2.31820 7.10779 1.55278 WAT0 198 0.00000
595 199 TIP3 OH2 1.12566 -7.19392 -0.25729 WAT0 199 0.00000
596 199 TIP3 H1 0.45134 -7.82336 -0.00171 WAT0 199 0.00000
597 199 TIP3 H2 1.68958 -7.67803 -0.86050 WAT0 199 0.00000
598 200 TIP3 OH2 6.26838 -9.08652 -0.14458 WAT0 200 0.00000
599 200 TIP3 H1 6.87214 -8.53898 -0.64648 WAT0 200 0.00000
600 200 TIP3 H2 5.39858 -8.76748 -0.38517 WAT0 200 0.00000
601 201 TIP3 OH2 7.99542 -7.94765 -1.81149 WAT0 201 0.00000
602 201 TIP3 H1 8.60717 -8.46208 -2.33813 WAT0 201 0.00000
603 201 TIP3 H2 8.37776 -7.07044 -1.78805 WAT0 201 0.00000
604 202 TIP3 OH2 -6.54759 -8.55989 -2.43530 WAT0 202 0.00000
605 202 TIP3 H1 -7.32461 -8.79440 -2.94271 WAT0 202 0.00000
606 202 TIP3 H2 -6.01723 -9.35668 -2.42650 WAT0 202 0.00000
607 203 TIP3 OH2 -7.71125 -8.76208 -6.63169 WAT0 203 0.00000
608 203 TIP3 H1 -7.27218 -8.15103 -7.22334 WAT0 203 0.00000
609 203 TIP3 H2 -8.34501 -8.22367 -6.15769 WAT0 203 0.00000
610 204 TIP3 OH2 -1.96833 -8.63318 -2.62199 WAT0 204 0.00000
611 204 TIP3 H1 -1.09399 -8.24475 -2.65156 WAT0 204 0.00000
612 204 TIP3 H2 -2.10425 -8.84840 -1.69927 WAT0 204 0.00000
613 205 TIP3 OH2 3.58851 -8.60320 -0.97282 WAT0 205 0.00000
614 205 TIP3 H1 3.66467 -8.50804 -1.92222 WAT0 205 0.00000
615 205 TIP3 H2 3.31343 -9.51091 -0.84391 WAT0 205 0.00000
616 206 TIP3 OH2 4.94177 -8.57742 -5.28032 WAT0 206 0.00000
617 206 TIP3 H1 4.23888 -7.96250 -5.49018 WAT0 206 0.00000
618 206 TIP3 H2 4.49691 -9.41475 -5.14923 WAT0 206 0.00000
619 207 TIP3 OH2 -7.81030 7.18614 -5.73418 WAT0 207 0.00000
620 207 TIP3 H1 -8.49531 7.14803 -6.40167 WAT0 207 0.00000
621 207 TIP3 H2 -7.80658 8.09890 -5.44597 WAT0 207 0.00000
622 208 TIP3 OH2 -5.85034 -6.84593 -8.18928 WAT0 208 0.00000
623 208 TIP3 H1 -5.35900 -7.47569 -8.71673 WAT0 208 0.00000
624 208 TIP3 H2 -5.22671 -6.54999 -7.52616 WAT0 208 0.00000
625 209 TIP3 OH2 -0.82433 -6.55278 -5.73223 WAT0 209 0.00000
626 209 TIP3 H1 -0.64620 -7.19946 -5.04937 WAT0 209 0.00000
627 209 TIP3 H2 -0.87771 -5.71901 -5.26512 WAT0 209 0.00000
628 210 TIP3 OH2 1.05405 8.39563 -7.33656 WAT0 210 0.00000
629 210 TIP3 H1 1.92007 8.76237 -7.51474 WAT0 210 0.00000
630 210 TIP3 H2 0.80733 7.95643 -8.15048 WAT0 210 0.00000
631 211 TIP3 OH2 7.76301 7.95866 -4.65745 WAT0 211 0.00000
632 211 TIP3 H1 7.56872 7.21087 -5.22249 WAT0 211 0.00000
633 211 TIP3 H2 7.72402 8.71667 -5.24066 WAT0 211 0.00000
634 212 TIP3 OH2 -6.58979 -8.04570 7.08232 WAT0 212 0.00000
635 212 TIP3 H1 -6.95597 -8.81144 7.52479 WAT0 212 0.00000
636 212 TIP3 H2 -5.67694 -8.01668 7.36883 WAT0 212 0.00000
637 213 TIP3 OH2 -4.61671 -8.69526 8.61803 WAT0 213 0.00000
638 213 TIP3 H1 -3.71835 -8.96924 8.43337 WAT0 213 0.00000
639 213 TIP3 H2 -5.00340 -9.43766 9.08229 WAT0 213 0.00000
640 214 TIP3 OH2 -5.99218 8.10622 -8.70897 WAT0 214 0.00000
641 214 TIP3 H1 -6.25972 8.39251 -7.83566 WAT0 214 0.00000
642 214 TIP3 H2 -5.22092 7.56014 -8.55672 WAT0 214 0.00000
643 215 TIP3 OH2 3.80452 -9.36273 8.80031 WAT0 215 0.00000
644 215 TIP3 H1 3.88124 -9.78866 9.65408 WAT0 215 0.00000
645 215 TIP3 H2 4.69818 -9.34926 8.45766 WAT0 215 0.00000
646 216 TIP3 OH2 6.98063 6.70990 7.49273 WAT0 216 0.00000
647 216 TIP3 H1 6.19882 6.52370 6.97279 WAT0 216 0.00000
648 216 TIP3 H2 6.90862 7.63933 7.70998 WAT0 216 0.00000


return





Posted by: tyrion_jj

Re: read-watbox.str - 03/20/19 10:24 PM

Dear Lennart,
I am a new about the charmm study, and I realy appreciate to you for professional and excellent scipts you provided, which is of great help for my study.
Recently, I met a severe problem that my atom numbers exceeds 100,000. I used your excellent script (solvent-box.str) but not worked. I want to know whether the 'read-watbox.str' script above applies to any systems. Because error would occur as below:
----------------------------------------
CHARMM> stream read-watbox.str
VOPEN> Attempting to open::read-watbox.str::
OPNLGU> Unit 98 opened for READONLY access to read-watbox.str

INPUT STREAM SWITCHING TO UNIT 98
RDTITL> 648
RDTITL> No title read.
Parameter: IN1 <- ""

CHARMM> 648

***** LEVEL 0 WARNING FROM *****
***** Unrecognized command: 648
******************************************
BOMLEV ( -2) IS NOT REACHED. WRNLEV IS 5


CHARMM> 1 1 TIP3 OH2 2.53067 0.59634 -2.47655 WAT0 1 0.00000

***** LEVEL 0 WARNING FROM *****
***** Unrecognized command: 1
******************************************
BOMLEV ( -2) IS NOT REACHED. WRNLEV IS 5

**** Warning **** The following extraneous characters
were found while command processing in CHARMM
1 TIP3 OH2 2.53067 0.59634 -2.47655 WAT0 1 0.00000
...
-------------------------------
And the same warnings are as the subsequnt 648 atoms. should I recreat a new box or ignore the warning?
Importantly, should the script 'solvent-box.str' you provided not modify anywhere?
Posted by: lennart

Re: read-watbox.str - 03/21/19 04:44 AM

It is not clear to me how the problem you describe is related to your having a system with more than 100 000 atoms.

It looks like the file read-watbox.str that you are using lacks the initial part:
*FILENAME: read-watbox.str
*PURPOSE: read 216 water molecule coord; used in solvation scripts
*AUTHOR: Lennart Nilsson, Karolinska Institutet, October 2003
read coor card resid
* This is a box of 216 3-site water molecules in the experimental
* geometry. It was constructed from an equilibrated
* configuration of TIP4P (4-site water model of Jorgenson)
* waters at 1 atm pressure and a density of 0.0334 molecules/A**-3.
* The box edgelength is 18.856 A. The minimum image periodic
* boundary energy for this configuration using the TIP4P
* potentials is -2150.6833 kcal/mol.
*

It is not supposed to edited.
Posted by: lennart

Re: read-watbox.str - 03/21/19 05:20 AM

It is not clear to me how the problem you describe is related to your having a system with more than 100 000 atoms.

It looks like the file read-watbox.str that you are using lacks the initial part:
*FILENAME: read-watbox.str
*PURPOSE: read 216 water molecule coord; used in solvation scripts
*AUTHOR: Lennart Nilsson, Karolinska Institutet, October 2003
read coor card resid
* This is a box of 216 3-site water molecules in the experimental
* geometry. It was constructed from an equilibrated
* configuration of TIP4P (4-site water model of Jorgenson)
* waters at 1 atm pressure and a density of 0.0334 molecules/A**-3.
* The box edgelength is 18.856 A. The minimum image periodic
* boundary energy for this configuration using the TIP4P
* potentials is -2150.6833 kcal/mol.
*

It is not supposed to be edited.
Posted by: tyrion_jj

Re: read-watbox.str - 03/21/19 06:52 AM

Hi Lennart,
Sorry, I misunderstood the script, I just want to delete some water molecules around enzyme rather than sovling my protein, sorry again! blush
Posted by: tyrion_jj

Re: read-watbox.str - 03/21/19 08:31 AM

Hi Lennart,
I found that the .crd file could not match the .psf file if the water molecules were above 9999. In addition, the sequence number in front of water molecule (in .psf file) will be re-coded from 1000 and more strangely the water molecules will change from the original three waters of a group to the thirty of a group. And that circumstance will also occur in .crd file, however, the water groups include 3 molecules (O,H,H) in the .pdb file. But in some big systems, the numbers of water molecule tent to exceed 9999, therefore, the error was occur. I would put some examples:
----------------------------------
pdb file:
ATOM 45562 OH2 TIP3 9998 67.087 105.130 87.105 1.00 0.00 SYS
ATOM 45563 H1 TIP3 9998 67.456 106.004 87.236 1.00 0.00 SYS
ATOM 45564 H2 TIP3 9998 67.169 104.705 87.958 1.00 0.00 SYS
ATOM 45565 OH2 TIP3 9999 8.307 61.746 93.842 1.00 0.00 SYS
ATOM 45566 H1 TIP3 9999 8.014 62.567 93.447 1.00 0.00 SYS
ATOM 45567 H2 TIP3 9999 9.023 61.452 93.279 1.00 0.00 SYS
ATOM 45568 OH2 TIP3 10000 8.247 90.174 65.975 1.00 0.00 SYS
ATOM 45569 H1 TIP3 10000 8.566 90.058 65.079 1.00 0.00 SYS
ATOM 45570 H2 TIP3 10000 9.014 90.469 66.465 1.00 0.00 SYS
ATOM 45571 OH2 TIP3 10001 31.001 88.714 55.161 1.00 0.00 SYS
ATOM 45572 H1 TIP3 10001 30.502 88.138 54.582 1.00 0.00 SYS
ATOM 45573 H2 TIP3 10001 30.878 88.341 56.034 1.00 0.00 SYS
ATOM 45574 OH2 TIP3 10002 8.114 38.241 100.338 1.00 0.00 SYS
ATOM 45575 H1 TIP3 10002 7.188 38.147 100.560 1.00 0.00 SYS
ATOM 45576 H2 TIP3 10002 8.360 37.392 99.970 1.00 0.00 SYS
ATOM 45577 OH2 TIP3 10003 18.070 12.027 102.139 1.00 0.00 SYS
ATOM 45578 H1 TIP3 10003 18.667 11.460 102.628 1.00 0.00 SYS
ATOM 45579 H2 TIP3 10003 17.835 12.718 102.758 1.00 0.00 SYS
ATOM 45580 OH2 TIP3 10004 66.462 68.942 36.977 1.00 0.00 SYS
ATOM 45581 H1 TIP3 10004 66.517 68.270 37.658 1.00 0.00 SYS
ATOM 45582 H2 TIP3 10004 66.069 68.493 36.229 1.00 0.00 SYS
ATOM 45583 OH2 TIP3 10005 1.460 76.054 55.401 1.00 0.00 SYS
ATOM 45584 H1 TIP3 10005 2.405 76.195 55.330 1.00 0.00 SYS
ATOM 45585 H2 TIP3 10005 1.304 75.949 56.339 1.00 0.00 SYS
ATOM 45586 OH2 TIP3 10006 38.244 85.145 53.199 1.00 0.00 SYS
ATOM 45587 H1 TIP3 10006 38.318 86.095 53.102 1.00 0.00 SYS
ATOM 45588 H2 TIP3 10006 39.145 84.845 53.312 1.00 0.00 SYS
ATOM 45589 OH2 TIP3 10007 34.853 111.818 89.479 1.00 0.00 SYS
ATOM 45590 H1 TIP3 10007 35.294 112.631 89.231 1.00 0.00 SYS
ATOM 45591 H2 TIP3 10007 35.124 111.185 88.814 1.00 0.00 SYS
ATOM 45592 OH2 TIP3 10008 90.960 84.284 103.726 1.00 0.00 SYS
ATOM 45593 H1 TIP3 10008 90.756 84.147 104.651 1.00 0.00 SYS
ATOM 45594 H2 TIP3 10008 91.906 84.435 103.709 1.00 0.00 SYS
ATOM 45595 OH2 TIP3 10009 0.454 85.368 72.956 1.00 0.00 SYS
ATOM 45596 H1 TIP3 10009 0.581 86.306 73.103 1.00 0.00 SYS
ATOM 45597 H2 TIP3 10009 0.694 85.236 72.038 1.00 0.00 SYS
ATOM 45598 OH2 TIP3 10010 77.891 35.326 105.254 1.00 0.00 SYS
ATOM 45599 H1 TIP3 10010 78.563 34.892 105.780 1.00 0.00 SYS


psf file:
45562 SYS 9998 TIP3 OH2 OW -0.834000 16.0000 0 0.00000 0.00000
45563 SYS 9998 TIP3 H1 HW 0.417000 1.00800 0 0.00000 0.00000
45564 SYS 9998 TIP3 H2 HW 0.417000 1.00800 0 0.00000 0.00000
45565 SYS 9999 TIP3 OH2 OW -0.834000 16.0000 0 0.00000 0.00000
45566 SYS 9999 TIP3 H1 HW 0.417000 1.00800 0 0.00000 0.00000
45567 SYS 9999 TIP3 H2 HW 0.417000 1.00800 0 0.00000 0.00000
45568 SYS 1000 TIP3 OH2 OW -0.834000 16.0000 0 0.00000 0.00000
45569 SYS 1000 TIP3 H1 HW 0.417000 1.00800 0 0.00000 0.00000
45570 SYS 1000 TIP3 H2 HW 0.417000 1.00800 0 0.00000 0.00000
45571 SYS 1000 TIP3 OH2 OW -0.834000 16.0000 0 0.00000 0.00000
45572 SYS 1000 TIP3 H1 HW 0.417000 1.00800 0 0.00000 0.00000
45573 SYS 1000 TIP3 H2 HW 0.417000 1.00800 0 0.00000 0.00000
45574 SYS 1000 TIP3 OH2 OW -0.834000 16.0000 0 0.00000 0.00000
45575 SYS 1000 TIP3 H1 HW 0.417000 1.00800 0 0.00000 0.00000
45576 SYS 1000 TIP3 H2 HW 0.417000 1.00800 0 0.00000 0.00000
45577 SYS 1000 TIP3 OH2 OW -0.834000 16.0000 0 0.00000 0.00000
45578 SYS 1000 TIP3 H1 HW 0.417000 1.00800 0 0.00000 0.00000
45579 SYS 1000 TIP3 H2 HW 0.417000 1.00800 0 0.00000 0.00000
45580 SYS 1000 TIP3 OH2 OW -0.834000 16.0000 0 0.00000 0.00000
45581 SYS 1000 TIP3 H1 HW 0.417000 1.00800 0 0.00000 0.00000
45582 SYS 1000 TIP3 H2 HW 0.417000 1.00800 0 0.00000 0.00000
45583 SYS 1000 TIP3 OH2 OW -0.834000 16.0000 0 0.00000 0.00000
45584 SYS 1000 TIP3 H1 HW 0.417000 1.00800 0 0.00000 0.00000
45585 SYS 1000 TIP3 H2 HW 0.417000 1.00800 0 0.00000 0.00000
45586 SYS 1000 TIP3 OH2 OW -0.834000 16.0000 0 0.00000 0.00000
45587 SYS 1000 TIP3 H1 HW 0.417000 1.00800 0 0.00000 0.00000
45588 SYS 1000 TIP3 H2 HW 0.417000 1.00800 0 0.00000 0.00000
45589 SYS 1000 TIP3 OH2 OW -0.834000 16.0000 0 0.00000 0.00000
45590 SYS 1000 TIP3 H1 HW 0.417000 1.00800 0 0.00000 0.00000
45591 SYS 1000 TIP3 H2 HW 0.417000 1.00800 0 0.00000 0.00000
45592 SYS 1000 TIP3 OH2 OW -0.834000 16.0000 0 0.00000 0.00000
45593 SYS 1000 TIP3 H1 HW 0.417000 1.00800 0 0.00000 0.00000
45594 SYS 1000 TIP3 H2 HW 0.417000 1.00800 0 0.00000 0.00000
45595 SYS 1000 TIP3 OH2 OW -0.834000 16.0000 0 0.00000 0.00000
45596 SYS 1000 TIP3 H1 HW 0.417000 1.00800 0 0.00000 0.00000
45597 SYS 1000 TIP3 H2 HW 0.417000 1.00800 0 0.00000 0.00000
45598 SYS 1001 TIP3 OH2 OW -0.834000 16.0000 0 0.00000 0.00000

crd file:
4556211025 TIP3 OH2 67.08707 105.13037 87.10451 SYS 9998 0.00000
4556311025 TIP3 H1 67.45643 106.00362 87.23586 SYS 9998 0.00000
4556411025 TIP3 H2 67.16915 104.70475 87.95793 SYS 9998 0.00000
4556511026 TIP3 OH2 8.30676 61.74561 93.84165 SYS 9999 0.00000
4556611026 TIP3 H1 8.01421 62.56709 93.44692 SYS 9999 0.00000
4556711026 TIP3 H2 9.02347 61.45160 93.27940 SYS 9999 0.00000
4556811027 TIP3 OH2 8.24731 90.17367 65.97459 SYS 1000 0.00000
4556911027 TIP3 H1 8.56581 90.05812 65.07936 SYS 1000 0.00000
4557011027 TIP3 H2 9.01416 90.46915 66.46536 SYS 1000 0.00000
4557111028 TIP3 OH2 31.00071 88.71445 55.16144 SYS 1000 0.00000
4557211028 TIP3 H1 30.50152 88.13846 54.58243 SYS 1000 0.00000
4557311028 TIP3 H2 30.87824 88.34116 56.03432 SYS 1000 0.00000
4557411029 TIP3 OH2 8.11393 38.24064 100.33772 SYS 1000 0.00000
4557511029 TIP3 H1 7.18755 38.14656 100.55953 SYS 1000 0.00000
4557611029 TIP3 H2 8.35954 37.39178 99.96983 SYS 1000 0.00000
4557711030 TIP3 OH2 18.07029 12.02655 102.13912 SYS 1000 0.00000
4557811030 TIP3 H1 18.66686 11.45996 102.62833 SYS 1000 0.00000
4557911030 TIP3 H2 17.83495 12.71777 102.75803 SYS 1000 0.00000
4558011031 TIP3 OH2 66.46179 68.94160 36.97731 SYS 1000 0.00000
4558111031 TIP3 H1 66.51686 68.27042 37.65755 SYS 1000 0.00000
4558211031 TIP3 H2 66.06859 68.49253 36.22902 SYS 1000 0.00000
4558311032 TIP3 OH2 1.46032 76.05442 55.40094 SYS 1000 0.00000
4558411032 TIP3 H1 2.40450 76.19495 55.33023 SYS 1000 0.00000
4558511032 TIP3 H2 1.30352 75.94866 56.33928 SYS 1000 0.00000
4558611033 TIP3 OH2 38.24374 85.14529 53.19886 SYS 1000 0.00000
4558711033 TIP3 H1 38.31828 86.09468 53.10215 SYS 1000 0.00000
4558811033 TIP3 H2 39.14538 84.84457 53.31217 SYS 1000 0.00000
4558911034 TIP3 OH2 34.85326 111.81799 89.47932 SYS 1000 0.00000
4559011034 TIP3 H1 35.29371 112.63063 89.23061 SYS 1000 0.00000
4559111034 TIP3 H2 35.12418 111.18541 88.81397 SYS 1000 0.00000
4559211035 TIP3 OH2 90.96047 84.28425 103.72593 SYS 1000 0.00000
4559311035 TIP3 H1 90.75630 84.14704 104.65099 SYS 1000 0.00000
4559411035 TIP3 H2 91.90560 84.43484 103.70903 SYS 1000 0.00000
4559511036 TIP3 OH2 0.45402 85.36834 72.95554 SYS 1000 0.00000
4559611036 TIP3 H1 0.58111 86.30550 73.10323 SYS 1000 0.00000
4559711036 TIP3 H2 0.69352 85.23578 72.03831 SYS 1000 0.00000
4559811037 TIP3 OH2 77.89127 35.32576 105.25352 SYS 1001 0.00000
4559911037 TIP3 H1 78.56271 34.89239 105.78040 SYS 1001 0.00000
--------------------------------------------
It is amazing....! It confused me..
Posted by: lennart

Re: read-watbox.str - 03/21/19 08:46 AM

Strange. A coordinate file and PSF created in the same job should match, unless you manipulate one of them before saving to disk.
I am not sure what you are doing, but I have no problem creating a system with more than 10000 water molecules.
PDB files have a numbering issue with more then 9999 residues, so it is usually easier to use CHARMM coordinate files, and only use PDB for export/import.
Are you using standard CHARMM and CHARMM toppar files? The TIP3P atom types in the CHARMM RTF/PARA files are OT and HT.

Post a simple input file which exhibits the problem.
Posted by: tyrion_jj

Re: read-watbox.str - 03/21/19 09:03 AM

Hi Lennart,
To be honest, my original .pdb, .psf and .crd files were transfored from Amber program. Then, I perfomed the below script to modify the format of these three files. This is my input script, I deleted 78342 atoms :
----------------------
* charmm input file for smll testsystem
*
bomblevel -1
wrnlev 5
prnlev 6

set jobname 19.9
set outjob mcp
set inputdir ./input
set topname ./toppar/parm14sb_all.rtf
set parname ./toppar/parm14sb_all.prm







! Topology files standard one
open read unit 1 card name @topname
read rtf card unit 1
close unit 1


! Parameter files
open read unit 2 card name @parname
read para card unit 2
close unit 2

!stream @{strname}


! psf file
open read unit 2 card name @{inputdir}/@{jobname}.psf
read psf card unit 2
close unit 2


open read form unit 13 name @{inputdir}/@{jobname}.crd
read coord card unit 13
close unit 13


!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
set safesphere 49
delete atom sort select .byres. -
( .not.( point 46. 57. 92. cut @safesphere ) -
.and. ( segid SYS .or. segid SSS) ) -
end
!delete atom sort select segid SSS end
!
JOIN SYS renu
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
IOFOrmat NOEXtended
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

open write card name ./@{outjob}.crd unit 41
write coordinates card select all end unit 41
* Coordinates after simulation of all atoms in protein,
* noextend crd format
*

open write card name ./@{outjob}.psf unit 49
write psf card unit 49
* This is the PSF for the structure of protein,
* noextend format
*

! Punch out the PDB
open write unit 19 card name ./@{outjob}.pdb
write coor pdb unit 19
* This is the PDB for the structure of PROTEIN
*
close unit 19

stop
---------------------------

Thank you for helping me! wink
Posted by: lennart

Re: read-watbox.str - 03/21/19 09:17 AM

As I said, do it all in CHARMM instead... and do not turn off the extended IOformat.
Posted by: tyrion_jj

Re: read-watbox.str - 03/21/19 09:39 AM

Hi lennart,
Thank you for your replying, I will perform your suggestion. Thank you again!