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标题: 使用GMX+CPK2跑QM/MM模拟，在生成GMX-cpk2模拟文件时，报原子没有QMMM原子序数错误。 [打印本页]

作者
Author: yjb 时间: 2021-12-31 13:56
标题: 使用GMX+CPK2跑QM/MM模拟，在生成GMX-cpk2模拟文件时，报原子没有QMMM原子序数错误。
使用GMX+CPK2跑QM/MM模拟，在生成GMX-cpk2模拟文件时，报原子没有QMMM原子序数错误。请问各位大神这个错误主要是怎么产生的，如何解决？
错误如下：

[jby@localhost test_water]$ gmx grompp -f md-qmmm.mdp -p topol.top -c md.gro -n index.ndx -o md_qmmm.tpr -maxwarn 10
   :-) GROMACS - gmx grompp, 2021.2-dev-UNCHECKED (double precision) (-:

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GROMACS:    gmx grompp, version 2021.2-dev-UNCHECKED (double precision)
Executable: /home/jby/soft/gromacs-2021.2-qmmm/build/bin/gmx_mpi_d
Data prefix:  /home/jby/soft/gromacs-2021.2-qmmm (source tree)
Working dir:  /home/jby/test_water
Command line:
  gmx_mpi_d grompp -f md-qmmm.mdp -p topol.top -c md.gro -n index.ndx -o md_qmmm.tpr -maxwarn 10

WARNING 1 [file md-qmmm.mdp]:
  Removing the rotation around the center of mass in a periodic system,
  this can lead to artifacts. Only use this on a single (cluster of)
  molecules. This cluster should not cross periodic boundaries.

Setting the LD random seed to 528479643

Generated 2556 of the 2556 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5

Generated 2556 of the 2556 1-4 parameter combinations

Excluding 3 bonded neighbours molecule type 'JZ4'

turning H bonds into constraints...

Excluding 2 bonded neighbours molecule type 'SOL'

turning H bonds into constraints...
Number of degrees of freedom in T-Coupling group QMatoms is 53.92
Number of degrees of freedom in T-Coupling group MMatoms is 4062.08

-------------------------------------------------------
Program:    gmx grompp, version 2021.2-dev-UNCHECKED
Source file: src/gromacs/applied_forces/qmmm/qmmmtopologypreprocessor.cpp (line 278)

Fatal error:
Atoms 0 does not have atomic number needed for QMMM. Check atomtypes section
in you topology or forcefield.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

作者
Author: 函数与激情 时间: 2022-11-26 22:57
Atoms 0 does not have atomic number needed for QMMM. Check atomtypes section
in you topology or forcefield.

hello, 我也遇到了同样的问题，请问你解决了吗？看不懂这个atom 0 表示啥意思。感觉可能是力场的原因，但是单独用gmx却可以打包成功。。。

作者
Author: yjb 时间: 2022-11-27 13:40

函数与激情发表于 2022-11-26 22:57
Atoms 0 does not have atomic number needed for QMMM. Check atomtypes section
in you topology or for ...

哈喽，这个问题当时我好像是手动修改了top文件的信息，自己手动加入了link atoms信息。之后就没有继续使用gmx+cp2k了，改用纯cp2k了

作者
Author: 函数与激情 时间: 2022-11-27 14:32

yjb 发表于 2022-11-27 13:40
哈喽，这个问题当时我好像是手动修改了top文件的信息，自己手动加入了link atoms信息。之后就没有继续使 ...

酱紫我来试试看十分感谢！

作者
Author: 大村驴 时间: 2025-2-9 17:32

函数与激情发表于 2022-11-26 22:57
Atoms 0 does not have atomic number needed for QMMM. Check atomtypes section
in you topology or for ...

有可能是你所用的原子类型问题，可以检查系统中第一个原子的原子类型，如果是gaff类型的，CP2K不认识，得用Amber类型

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