运行em.gro时离子和水无法形成一个文件

kellyisgood · 发表于 Post on 2022-12-21 17:32:18

运行命令：
gmx_mpi make_ndx -f em.gro -o index.ndx
报错提示：

Jotaro · 发表于 Post on 2022-12-21 20:51:04

gro文件发一下

kellyisgood · 发表于 Post on 2022-12-21 20:58:19

Jotaro 发表于 2022-12-21 20:51
gro文件发一下

Protein in water
75601
7GLN    N 1 8.947 7.996 1.766
7GLN    H1 2 9.003 8.077 1.728
7GLN    H2 3 8.855 7.998 1.718
7GLN    H3 4 8.930 8.015 1.866
7GLN    CA 5 9.017 7.865 1.746
7GLN    HA 6 9.043 7.857 1.642
7GLN    CB 7 9.145 7.861 1.834
7GLN HB1 8 9.187 7.758 1.837
7GLN HB2 9 9.117 7.884 1.939
7GLN    CG 10 9.260 7.956 1.791
7GLN HG1 11 9.343 7.948 1.865
7GLN HG2 12 9.225 8.062 1.791
7GLN    CD 13 9.317 7.922 1.653
7GLN OE1 14 9.287 7.818 1.594
7GLN NE2 15 9.400 8.012 1.596
7GLN HE21 16 9.420 8.099 1.640
7GLN HE22 17 9.448 7.986 1.511
7GLN    C 18 8.921 7.751 1.775
7GLN    O 19 8.803 7.775 1.797
8GLN    N 20 8.965 7.623 1.772
8GLN    HN 21 9.062 7.599 1.763
8GLN    CA 22 8.880 7.513 1.814
8GLN    HA 23 8.812 7.547 1.892
8GLN    CB 24 8.802 7.441 1.699
8GLN HB1 25 8.731 7.370 1.749
8GLN HB2 26 8.872 7.379 1.638
8GLN    CG 27 8.718 7.531 1.604
8GLN HG1 28 8.664 7.607 1.663
8GLN HG2 29 8.640 7.466 1.558
8GLN    CD 30 8.797 7.592 1.489
"em.gro" 75604L, 3402159C

请帮忙看一下，谢谢！

Jotaro · 发表于 Post on 2022-12-21 21:00:12

kellyisgood 发表于 2022-12-21 20:58
Protein in water
75601
7GLN N 1 8.947 7.996 1.766

我的意思是，发一下文件

kellyisgood · 发表于 Post on 2022-12-21 21:26:17

Jotaro 发表于 2022-12-21 21:00
我的意思是，发一下文件

不好意思老师我好像传不了那个文件以上是em.gro文件里的全部内容

Jotaro · 发表于 Post on 2022-12-21 21:30:30

kellyisgood 发表于 2022-12-21 21:26
不好意思老师我好像传不了那个文件以上是em.gro文件里的全部内容

看看新人必读里怎么传文件，gro不能就这几十行

kellyisgood · 发表于 Post on 2022-12-21 21:40:16

Jotaro 发表于 2022-12-21 21:30
看看新人必读里怎么传文件，gro不能就这几十行

复制到文档里了老师您在帮忙看一下吧

Jotaro · 发表于 Post on 2022-12-21 21:52:47

我用sob老师预编译的Gromacs 2020.6在windows下可以正常生成。

kellyisgood · 发表于 Post on 2022-12-21 22:28:58

Jotaro 发表于 2022-12-21 21:52
我用sob老师预编译的Gromacs 2020.6在windows下可以正常生成。

啊那是我自己装的gromacs的问题吗
还是我缺少什么文件呀

Jotaro · 发表于 Post on 2022-12-21 22:32:57

kellyisgood 发表于 2022-12-21 22:28
啊那是我自己装的gromacs的问题吗
还是我缺少什么文件呀

直接在windows下用sob老师预编译好的做index文件

kellyisgood · 发表于 Post on 2022-12-21 22:42:59

Jotaro 发表于 2022-12-21 22:32
直接在windows下用sob老师预编译好的做index文件

有在linux上用的满？可以分享一下吗

Jotaro · 发表于 Post on 2022-12-21 23:04:28

kellyisgood 发表于 2022-12-21 22:42
有在linux上用的满？可以分享一下吗

linux自己编译，一般不会出问题

kellyisgood · 发表于 Post on 2022-12-22 10:25:25

本帖最后由 kellyisgood 于 2022-12-22 10:34 编辑

Jotaro 发表于 2022-12-21 22:32
直接在windows下用sob老师预编译好的做index文件

好的老师，谢谢解答。目前我的水和离子还是无法形成一个文件，是我的index文件有问题吗

牧生 · 发表于 Post on 2022-12-22 10:45:35

一切操作正常，2019.6

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:    gmx make_ndx, version 2019.6
Executable: D:\gmx2019.6_win64_GPU\gmx2019.6_GPU\bin\gmx.exe
Data prefix:  D:\gmx2019.6_win64_GPU\gmx2019.6_GPU
Working dir:  C:\Users\Administrator\Desktop
Command line:
  gmx make_ndx -f em.gro -o index.ndx

Reading structure file
Going to read 0 old index file(s)
Analysing residue names:
There are: 459 Protein residues
There are:    9    Other residues
There are: 22791    Water residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...

  0 System             : 75601 atoms
  1 Protein          :  7044 atoms
  2 Protein-H          :  3548 atoms
  3 C-alpha          : 459 atoms
  4 Backbone          :  1377 atoms
  5 MainChain          :  1835 atoms
  6 MainChain+Cb       :  2259 atoms
  7 MainChain+H       :  2273 atoms
  8 SideChain          :  4771 atoms
  9 SideChain-H       :  1713 atoms
10 Prot-Masses       :  7044 atoms
11 non-Protein       : 68557 atoms
12 Other             : 184 atoms
13 UNK0             : 176 atoms
14 SOD                :    8 atoms
15 Water             : 68373 atoms
16 SOL                : 68373 atoms
17 non-Water          :  7228 atoms

nr : group    '!': not  'name' nr name 'splitch' nr Enter: list groups
'a': atom    '&': and  'del' nr       'splitres' nr 'l': list residues
't': atom type  '|': or 'keep' nr       'splitat' nr 'h': help
'r': residue             'res' nr       'chain' char
"name": group          'case': case sensitive          'q': save and quit
'ri': residue index

> 1|13

Copied index group 1 'Protein'
Copied index group 13 'UNK0'
Merged two groups with OR: 7044 176 -> 7220

18 Protein_UNK0       :  7220 atoms

> 14|15

Copied index group 14 'SOD'
Copied index group 15 'Water'
Merged two groups with OR: 8 68373 -> 68381

19 SOD_Water          : 68381 atoms

kellyisgood · 发表于 Post on 2022-12-22 17:00:46

牧生发表于 2022-12-22 10:45
一切操作正常，2019.6

Copyright (c) 1991-2000, University of Groningen, The Netherlands.

好奇怪，刚刚试了一下还是如下报错
Copied index group 14 'SOD'
Copied index group 15 'Water'
One of your groups is not ascending
Group is empty

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[GROMACS] 运行em.gro时离子和水无法形成一个文件

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