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各位老师好，我在尝试用gromacs2024.5做蛋白-配体的分子动力学模拟。
蛋白配体的结构文件使用的是Desmond模拟300ns后最后一帧的结构，对于蛋白文件，用gmx pdb2gmx -f protein.pdb -o protein.gro -ignh命令处理（因为是测试，力场瞎选的）；对于配体，用sobtop处理，将配体的文件合并到top文件后，依次使用如下命令：
gmx editconf -f complex.gro -o complex_box.gro -bt cubic -box 10 10 10
gmx solvate -cp complex_box.gro -o complex_sol.gro -p topol.top
gmx grompp -f em.mdp -c complex_sol.gro -p topol.top -o em.tpr -maxwarn 2
这个命令打完之后报WARNING 2 [file em.mdp]:
The largest distance between excluded atoms is 1.504 nm between atom 8576
and 8585, which is larger than the cut-off distance. This will lead to
missing long-range corrections in the forces and energies. If you expect
that minimization will bring such distances within the cut-off, you can
ignore this warning.
gmx genion -s em.tpr -p topol.top -o system.gro -neutral
gmx grompp -f em.mdp -c system.gro -p topol.top -o em.tpr -maxwarn 1
gmx mdrun -v -deffnm em -pin on -notunepme -ntmpi 1 -ntomp 12
这里输出
Polak-Ribiere Conjugate Gradients converged to machine precision in 193 steps,
but did not reach the requested Fmax < 100.
Potential Energy = 3.1468682e+08
Maximum force = 1.3912910e+09 on atom 20458
Norm of force = 6.3254481e+06
gmx grompp -f pr.mdp -c em.gro -p topol.top -r em.gro -o pr.tpr
这里输出
ERROR 1 [file pr.mdp]:
The largest distance between excluded atoms is 6.952 nm between atom 7246
and 7261, which is larger than the cut-off distance. This will lead to
missing long-range corrections in the forces and energies.
Fatal error:
There was 1 error in input file(s)
请问各位老师这是因为什么呢，换gromacs2023.2版本也报错，bash的日志和运行文件都上传了；恳请各位老师指点！
bash.txt
(63.38 KB, 下载次数 Times of downloads: 0)
gmx-file.zip
(4.44 MB, 下载次数 Times of downloads: 2)
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发表于 Post on 2025-7-8 14:46:21
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发表于 Post on 2025-7-9 05:34:31
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