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标题: 求助top文件和gro文件的atom name不匹配 [打印本页]

作者
Author: phosphorescence 时间: 2024-5-13 09:31
标题: 求助top文件和gro文件的atom name不匹配
各位老师好，
我是使用高斯16优化的单分子，保存成了pdb文件和mol2文件。使用pdb文件在Packmol中建立了一个5*5*5共50个分子的模型，使用mol2文件在sobtop文件中生成了itp和top文件。运行的时候，提醒top文件中和gro文件中的原子名称不匹配。检查了两个文件，原子信息是一直的，忽略了waring，但还是继续报错，不知道应该怎么办。
具体报错信息如下：

  gmx grompp -f em.mdp -c NZ2TPA_50.gro -p NZ2TPA.top -o em.tpr -maxwarn 1

Setting the LD random seed to 1052438418
Generated 21 of the 21 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 21 of the 21 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'S0'
Warning: atom name 1 in NZ2TPA.top and NZ2TPA_50.gro does not match (C1 - C)
Warning: atom name 2 in NZ2TPA.top and NZ2TPA_50.gro does not match (C2 - C)
Warning: atom name 3 in NZ2TPA.top and NZ2TPA_50.gro does not match (C3 - C)
Warning: atom name 4 in NZ2TPA.top and NZ2TPA_50.gro does not match (C4 - C)
Warning: atom name 5 in NZ2TPA.top and NZ2TPA_50.gro does not match (C5 - C)
Warning: atom name 6 in NZ2TPA.top and NZ2TPA_50.gro does not match (C6 - C)
Warning: atom name 7 in NZ2TPA.top and NZ2TPA_50.gro does not match (C7 - C)
Warning: atom name 8 in NZ2TPA.top and NZ2TPA_50.gro does not match (C8 - C)
Warning: atom name 9 in NZ2TPA.top and NZ2TPA_50.gro does not match (C9 - C)
Warning: atom name 10 in NZ2TPA.top and NZ2TPA_50.gro does not match (C10 - C)
Warning: atom name 11 in NZ2TPA.top and NZ2TPA_50.gro does not match (C11 - C)
Warning: atom name 12 in NZ2TPA.top and NZ2TPA_50.gro does not match (C12 - C)
Warning: atom name 13 in NZ2TPA.top and NZ2TPA_50.gro does not match (C13 - C)
Warning: atom name 14 in NZ2TPA.top and NZ2TPA_50.gro does not match (C14 - C)
Warning: atom name 15 in NZ2TPA.top and NZ2TPA_50.gro does not match (C15 - C)
Warning: atom name 16 in NZ2TPA.top and NZ2TPA_50.gro does not match (C16 - C)
Warning: atom name 17 in NZ2TPA.top and NZ2TPA_50.gro does not match (C17 - C)
Warning: atom name 18 in NZ2TPA.top and NZ2TPA_50.gro does not match (C18 - C)
Warning: atom name 19 in NZ2TPA.top and NZ2TPA_50.gro does not match (N19 - N)
Warning: atom name 20 in NZ2TPA.top and NZ2TPA_50.gro does not match (C20 - C)
(more than 20 non-matching atom names)

WARNING 1 [file NZ2TPA.top, line 14]:
  4150 non-matching atom names
  atom names from NZ2TPA.top will be used
  atom names from NZ2TPA_50.gro will be ignored

作者
Author: sobereva 时间: 2024-5-14 08:03
-maxwarn加上超过warning数的数值忽略就完了
不需要拓扑文件和结构文件的原子名对应，只需要顺序对应

作者
Author: yql 时间: 2025-2-10 10:53
在gromacs上把pdb文件转换为gro，再转换为pdb应该就可以了

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