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gromacs示例求助

作者 Mr_ANZ
来源: 小木虫 600 12 举报帖子
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如题,gromacs中文教程初学者,做溶菌酶那个到nvt平衡那一步产生tpr文件时老是出错,具体如下,求大佬指点一下,,,
Command line:
  gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr

Ignoring obsolete mdp entry 'title'
Setting the LD random seed to 1818880411
Generated 330891 of the 330891 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 330891 of the 330891 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'CL'
turning all bonds into constraints...
Setting gen_seed to -691171019
Velocities were taken from a Maxwell distribution at 300 K
Removing all charge groups because cutoff-scheme=Verlet

-------------------------------------------------------
Program:     gmx grompp, version 2018.1
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2008)

Fatal error:
Cannot find position restraint file restraint.gro (option -r).
From GROMACS-2018, you need to specify the position restraint coordinate files
explicitly to avoid mistakes, although you can still use the same file as you
specify for the -c option.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors 返回小木虫查看更多

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  • 112233ssg

    所加原子的个数和top里面的数量没对应上,可能有些分子没加进去,在加分子时的命令上最后用try试试

  • gmx模拟

    少一个限制文件,看错误提示就知道那个限制文件(restraint.gro),这个文件需要在你当前目录下,详细的你可以根据提示去去网站上找错误的原因和解决方法,都有的,多看错误提示(Fatal error:后面的内容),看不到复制翻译下,

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