24小时热门版块排行榜

返回列表

kangsgo

新虫 (初入文坛)

应助: 0 (幼儿园)
金币: 93.6
帖子: 19
在线: 15.9小时
虫号: 2389350
注册: 2013-03-30
专业: 蛋白质组学

[求助] gromacs配体力场电荷的问题

我先教程在线服务器PRODRG 2.5的方法建立的力场电荷文件如下：

引用回帖:

; nr    type  resnr resid  atom  cgnr charge    mass

   1    CH2    1  EVO    CAF    1 0.000  13.0190

   2       C    1  EVO    CAE    2 0.023  12.0110

   3       NR    1  EVO    NAC    2 0.043  14.0067

   4       H    1  EVO    HAC    2 -0.066 1.0080

   5       C    1  EVO    CAI    3 0.116  12.0110

   6    CR1    1  EVO    CAP    3 -0.022  12.0110

   7       HC    1  EVO    HAR    3 0.011 1.0080

   8    CR1    1  EVO    CAU    3 -0.022  12.0110

   9       HC    1  EVO    HAY    3 0.011 1.0080

10    CR1    1  EVO    CAT    3 -0.022  12.0110

11       HC    1  EVO    HAX    3 0.011 1.0080

12    CR1    1  EVO    CAO    3 -0.022  12.0110

13       HC    1  EVO    HAQ    3 0.011 1.0080

14       C    1  EVO    CAH    3 -0.036  12.0110

15       C    1  EVO    CAG    3 -0.036  12.0110

16    CH2    1  EVO    CAM    4 0.113  14.0270

17    CH1    1  EVO    CAN    4 0.112  14.0270

18       NL    1  EVO    NAB    4 0.773  14.0067

19       OA    1  EVO    OAA    4 -0.160  15.9994

20    CH2    1  EVO    CAJ    4 0.162  13.0190

21       C    1  EVO    CAL    5 -0.016  12.0110

22    CR1    1  EVO    CAR    5 -0.009  12.0110

23       HC    1  EVO    HAT    5 0.025 1.0080

24    CR1    1  EVO    CAW    6 -0.015  12.0110

25       HC    1  EVO    HA0    6 0.015 1.0080

26    CR1    1  EVO    CAV    6 -0.015  12.0110

27       HC    1  EVO    HAZ    6 0.015 1.0080

28    CR1    1  EVO    CAQ    7 -0.016  12.0110

29       HC    1  EVO    HAS    7 0.013 1.0080

30       C    1  EVO    CAK    7 0.145  12.0110

31       NL    1  EVO    NAD    7 -0.236  14.0067

32    CH3    1  EVO    CAS    7 0.094  15.0350

群里和教程说这个做出来不准，用ATB较好，于是我用它做了一个，如下：

引用回帖:

[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  charge mass total_charge
1 HC 1 SDSG H13 1 0.089 1.0080
2    C 1 SDSG C15 1 -0.127  12.0110
3 HC 1 SDSG H11 1 0.089 1.0080
4 HC 1 SDSG H12 1 0.089 1.0080    ;  0.140
5 NT 1 SDSG    N3 2 -0.530  14.0067
6    C 1 SDSG    C2 2 0.710  12.0110
7 HC 1 SDSG    H2 2 0.035 1.0080
8    C 1 SDSG    C1 2 -0.239  12.0110
9 NT 1 SDSG    N2 2 -0.437  14.0067
10  HS14 1 SDSG    H1 2 0.364 1.0080
11    C 1 SDSG    C3 2 0.097  12.0110    ; -0.000
12    C 1 SDSG    C5 3 0.309  12.0110
13    C 1 SDSG    C4 3 -0.122  12.0110
14    C 1 SDSG C12 3 -0.372  12.0110
15 HC 1 SDSG    H8 3 0.185 1.0080    ;  0.000
16    C 1 SDSG C11 4 -0.139  12.0110
17 HC 1 SDSG    H7 4 0.139 1.0080    ;  0.000
18    C 1 SDSG C16 5 -0.223  12.0110
19 HC 1 SDSG H14 5 0.171 1.0080
20    C 1 SDSG C17 5 -0.068  12.0110
21 HC 1 SDSG H15 5 0.120 1.0080    ;  0.000
22    C 1 SDSG    C7 6 0.552  12.0110
23    C 1 SDSG    C8 6 -0.355  12.0110
24    C 1 SDSG C13 6 -0.383  12.0110
25 HC 1 SDSG    H9 6 0.186 1.0080    ;  0.000
26    C 1 SDSG C14 7 -0.023  12.0110
27 HC 1 SDSG H10 7 0.109 1.0080
28    C 1 SDSG C19 7 -0.216  12.0110
29 HC 1 SDSG H17 7 0.130 1.0080    ;  0.000
30    C 1 SDSG C18 8 -0.012  12.0110
31 HC 1 SDSG H16 8 0.149 1.0080    ;  0.137
32 NT 1 SDSG    N1 9 -0.560  14.0067
33    C 1 SDSG    C6 9 0.704  12.0110
34    O 1 SDSG    O1 9 -0.589  15.9994
35    C 1 SDSG C10 9 -0.019  12.0110
36 HC 1 SDSG    H5 9 0.079 1.0080
37 HC 1 SDSG    H6 9 0.108 1.0080    ; -0.277
38    C 1 SDSG    C9 10 -0.188  12.0110
39 HC 1 SDSG    H3 10 0.096 1.0080
40 HC 1 SDSG    H4 10 0.092 1.0080    ;  0.000
; total charge of the molecule:  -0.000

但是它为何有两个的原子数都不相同·····所以我又用gaussian和ambertools做了一下resp，电荷如下：

引用回帖:

1  DUMM  DU M 0  -1  -2    0.000    .0       .0    .00000
2  DUMM  DU M 1 0  -1    1.449    .0       .0    .00000
3  DUMM  DU M 2 1 0    1.523 111.21    .0    .00000
4  C18 ca M 3 2 1    1.540 111.208  -180.000 -0.055157
5  C19 ca B 4 3 2    1.386 85.241 142.707 -0.250863
6  C14 ca B 5 4 3    1.382 118.685 127.363 -0.013132
7  C8 ca S 6 5 4    1.388 120.843    0.144 -0.295655
8  C6 c    S 7 6 5    1.484 118.878  -177.881  0.775848
9  O1 o    E 8 7 6    1.202 122.075    1.441 -0.589377
10  H10 ha E 6 5 4    1.073 121.147  -179.133  0.138140
11  H17 ha E 5 4 3    1.075 120.678 -52.361  0.151555
12  H16 ha E 4 3 2    1.076 61.050 14.700  0.143398
13  C13 ca M 4 3 2    1.383 124.432 -92.009 -0.348872
14  H9 ha E 13 4 3    1.072 119.445 73.243  0.169709
15  C7 ca M 13 4 3    1.397 119.914  -107.315  0.407232
16  N3 nh M 15  13 4    1.380 122.608 178.980 -0.314454
17  C15 c3 3 16  15  13    1.443 121.147 -10.183 -0.164667
18  H11 h1 E 17  16  15    1.081 109.161  -168.263  0.088033
19  H12 h1 E 17  16  15    1.083 110.363 -49.702  0.088033
20  H13 h1 E 17  16  15    1.089 113.402 71.436  0.088033
21  C2 c3 M 16  15  13    1.440 119.011 159.869  0.137290
22  H2 h2 E 21  16  15    1.083 106.205 157.152  0.153836
23  N1 n    M 21  16  15    1.454 111.980 41.122 -0.499094
24  C10 c3 M 23  21  16    1.462 112.625 176.392  0.087076
25  H5 h1 E 24  23  21    1.085 107.153 -53.056  0.061913
26  H6 h1 E 24  23  21    1.077 108.409  -169.658  0.061913
27  C9 c3 M 24  23  21    1.537 111.448 67.415 -0.224694
28  H3 hc E 27  24  23    1.087 109.239  -162.305  0.111802
29  H4 hc E 27  24  23    1.086 109.717 80.840  0.111802
30  C3 cd M 27  24  23    1.505 109.472 -40.598 -0.034776
31  C1 cc M 30  27  24    1.347 123.077 10.717  0.145019
32  N2 na M 31  30  27    1.378 110.755  -177.270 -0.671235
33  H1 hn E 32  31  30    0.993 124.025  -160.962  0.437444
34  C5 ca M 32  31  30    1.377 107.985 -3.570  0.344809
35  C4 ca M 34  32  31    1.401 108.072    3.182 -0.053032
36  C11 ca M 35  34  32    1.397 119.313 178.515 -0.134838
37  H7 ha E 36  35  34    1.075 120.594  -179.623  0.143002
38  C16 ca M 36  35  34    1.377 118.987    0.732 -0.233578
39  H14 ha E 38  36  35    1.076 119.885 179.756  0.152162
40  C17 ca M 38  36  35    1.402 120.836 -0.091 -0.098966
41  H15 ha E 40  38  36    1.075 119.352 179.829  0.139658
42  C12 ca M 40  38  36    1.377 121.238 -0.370 -0.326357
43  H8 ha E 42  40  38    1.076 121.084  -179.649  0.171039

所以我有点迷茫了···我应该如何将其后面生成的电荷给转入进去呀？

回复此楼

» 猜你喜欢

1楼 2015-11-11 23:11:22

已阅回复此楼关注TA 给TA发消息送TA红花 TA的回帖

相关版块跳转我要订阅楼主 kangsgo 的主题更新

返回列表