能量最小化生成tpr文件时，报错显示top与gro文件中的CL与CLA原子不匹配

LvYang · 发表于 Post on 2022-10-23 22:55:11

指令：gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr
报错：Excluding 3 bonded neighbours molecule type 'CL'
Warning: atom name 33489 in topol.top and solv_ions.gro does not match (CLA - CL)
Warning: atom name 33490 in topol.top and solv_ions.gro does not match (CLA - CL)
Warning: atom name 33491 in topol.top and solv_ions.gro does not match (CLA - CL)
Warning: atom name 33492 in topol.top and solv_ions.gro does not match (CLA - CL)
Warning: atom name 33493 in topol.top and solv_ions.gro does not match (CLA - CL)
Warning: atom name 33494 in topol.top and solv_ions.gro does not match (CLA - CL)

WARNING 1 [file topol.top, line 24633]:
  6 non-matching atom names
  atom names from topol.top will be used
  atom names from solv_ions.gro will be ignored

Analysing residue names:
There are: 163 Protein residues
There are:    7    Other residues
There are: 10284    Water residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group rest is 69627.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 72x72x72, spacing 0.109 0.109 0.109
Estimate for the relative computational load of the PME mesh part: 0.22
This run will generate roughly 3 Mb of data
我从top文件中molecules里找到了6个CL，但是atoms内容中未找到CLA分子到底在哪里；通过更改gro文件中的CL为CLA无法解决该问题，我该如何从top文件中查到CLA原子使其与gro文件中的CL匹配呢？

solv_ions.zip (384.83 KB, 下载次数 Times of downloads: 2)

topol.zip (95.46 KB, 下载次数 Times of downloads: 1)

sobereva · 发表于 Post on 2022-10-24 05:27:15

gro和拓扑文件里原子名不匹配没关系，顺序对应即可
CLA是#include "./charmm36.ff/ions.itp"里的氯离子的原子名

LvYang · 发表于 Post on 2022-10-24 17:14:28

sobereva 发表于 2022-10-24 05:27
gro和拓扑文件里原子名不匹配没关系，顺序对应即可
CLA是#include "./charmm36.ff/ions.itp"里的氯离子的 ...

感谢sob老师！我从力场文件夹下的ions.itp文件中找到了对氯原子的命名，并将itp文件中的CLA改为CL解决了该问题！

wyfgg · 发表于 Post on 2022-12-8 14:03:18

LvYang 发表于 2022-10-24 17:14
感谢sob老师！我从力场文件夹下的ions.itp文件中找到了对氯原子的命名，并将itp文件中的CLA改为CL解决了 ...

按理说，你不应该修改力场文件内的原子类型名称，直接加个-maxwarn 1就好了

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[GROMACS] 能量最小化生成tpr文件时，报错显示top与gro文件中的CL与CLA原子不匹配

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