计算化学公社

标题: acpype执行命令报错 [打印本页]

作者
Author: the_best_luck 时间: 2023-12-19 10:46
标题: acpype执行命令报错
（1）报错内容如图所示：

（2）分子结构如图

分子mol2文件内容：
@<TRIPOS>MOLECULE
6
41 43 0 0 0
SMALL
GASTEIGER

@<TRIPOS>ATOM
   1 C       10.9783 7.8593 15.2443 C.3    1  SUB1    -0.0384
   2 C          9.5661 7.9825 15.8314 C.3    1  SUB1    -0.0289
   3 C          9.1414 7.1025 16.8730 C.3    1  SUB1       0.0260
   4 C          9.9847 6.0460 17.5029 C.2    1  SUB1       0.1958
   5 O       10.4082 6.1898 18.6507 O.2    1  SUB1    -0.2866
   6 C       10.1920 4.7974 16.7217 C.3    1  SUB1       0.0523
   7 C       10.0904 4.6477 15.3134 C.3    1  SUB1       0.0596
   8 N       10.3415 3.4054 14.9246 N.pl3 1  SUB1    -0.1797
   9 N       10.5875 2.7191 16.0630 N.pl3 1  SUB1    -0.2811
   10 C       10.8671 1.2977 15.9972 C.3    1  SUB1       0.0295
   11 C       10.5040 3.5439 17.1687 C.3    1  SUB1    -0.0036
   12 O       10.6929 3.0690 18.4162 O.co2 1  SUB1    -0.8599
   13 C          7.8468 7.2259 17.4042 C.3    1  SUB1    -0.0488
   14 C          6.9697 8.2048 16.9246 C.3    1  SUB1    -0.0356
   15 C          7.3645 9.1020 15.9139 C.3    1  SUB1       0.0971
   16 S          6.1022 10.3184 15.4238 S.O2 1  SUB1    -0.0053
   17 C          5.2024 9.5279 14.0291 C.3    1  SUB1       0.0596
   18 O          5.1360 10.4386 16.5249 O.2    1  SUB1    -0.1696
   19 O          6.7480 11.5428 14.9272 O.2    1  SUB1    -0.1696
   20 C          8.6695 8.9916 15.3445 C.3    1  SUB1       0.0279
   21 C          9.1207 9.9211 14.2679 C.2    1  SUB1       0.0925
   22 N       10.1112 10.7037 14.3835 N.2    1  SUB1    -0.0889
   23 O       10.3564 11.3453 13.1473 O.2    1  SUB1    -0.3932
   24 C          9.7109 10.5864 12.1354 C.3    1  SUB1       0.1234
   25 C          8.5552 9.9800 12.8863 C.3    1  SUB1       0.0302
   26 H       10.9335 7.7545 14.1555 H    1  SUB1       0.0278
   27 H       11.5694 8.7430 15.4861 H    1  SUB1       0.0278
   28 H       11.5411 7.0090 15.6205 H    1  SUB1       0.0278
   29 H          9.8563 5.3859 14.5621 H    1  SUB1       0.0855
   30 H          9.9970 0.7445 16.3531 H    1  SUB1       0.0472
   31 H       11.0870 0.9957 14.9722 H    1  SUB1       0.0472
   32 H       11.7261 1.0632 16.6268 H    1  SUB1       0.0472
   33 H          7.5114 6.5644 18.1904 H    1  SUB1       0.0625
   34 H          5.9793 8.2635 17.3505 H    1  SUB1       0.0637
   35 H          4.4200 10.2055 13.6867 H    1  SUB1       0.0468
   36 H          5.8800 9.2986 13.2119 H    1  SUB1       0.0468
   37 H          4.7454 8.6060 14.3852 H    1  SUB1       0.0468
   38 H       10.3773 9.8109 11.7485 H    1  SUB1       0.0727
   39 H          9.3838 11.2314 11.3244 H    1  SUB1       0.0727
   40 H          8.2739 9.0043 12.5031 H    1  SUB1       0.0363
   41 H          7.6976 10.6475 12.8437 H    1  SUB1       0.0363
@<TRIPOS>BOND
   1    1    2 1
   2    1 26 1
   3    1 27 1
   4    1 28 1
   5    2    3 ar
   6    2 20 ar
   7    3    4 1
   8    3 13 ar
   9    4    5 2
10    4    6 1
11    6    7 ar
12    6 11 ar
13    7    8 ar
14    7 29 1
15    8    9 ar
16    9 10 1
17    9 11 ar
18 10 30 1
19 10 31 1
20 10 32 1
21 11 12 1
22 13 14 ar
23 13 33 1
24 14 15 ar
25 14 34 1
26 15 16 1
27 15 20 ar
28 16 17 1
29 16 18 2
30 16 19 2
31 17 35 1
32 17 36 1
33 17 37 1
34 20 21 1
35 21 22 2
36 21 25 1
37 22 23 1
38 23 24 1
39 24 25 1
40 24 38 1
41 24 39 1
42 25 40 1
43 25 41 1

看着分子结构都是正常的，还麻烦大佬们帮忙看下。
我太菜鸡了，今年还错过了gromacs培训，明年上半年一定要抓住！

作者
Author: sobereva 时间: 2023-12-19 12:49
用sobtop（http://sobereva.com/soft/Sobtop）产生拓扑文件多好
各种acpype的破毛病都没有，普适得多得多得多

作者
Author: the_best_luck 时间: 2024-1-3 12:35

sobereva 发表于 2023-12-19 12:49
用sobtop（http://sobereva.com/soft/Sobtop）产生拓扑文件多好
各种acpype的破毛病都没有，普适得多得多 ...

谢谢谢谢

欢迎光临计算化学公社 (http://bbs.keinsci.com/)