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我在使用的charmm力场中的aminoacids.rtp中发现了最开始认为的非标准氨基酸残基PTR,通过对比初始蛋白文件，发现在该位置的原子名称与aminoacids.rtp中的其中一个原子名称对应不上，于是修改蛋白文件里的原子名称与rtp文件中保持一致，结果可以运行，于是接着往下走。同样遇到了这个能量最小化的问题：
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 50000
Step= 0, Dmax= 1.0e-02 nm, Epot= 8.93542e+16 Fmax= inf, atom= 7370
Step= 14, Dmax= 1.2e-06 nm, Epot= 8.93542e+16 Fmax= inf, atom= 7370
Energy minimization has stopped because the force on at least one atom is not
finite. This usually means atoms are overlapping. Modify the input
coordinates to remove atom overlap or use soft-core potentials with the free
energy code to avoid infinite forces.
You could also be lucky that switching to double precision is sufficient to
obtain finite forces.
writing lowest energy coordinates.
Back Off! I just backed up em.gro to ./#em.gro.1#
Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = 8.9354175e+16
Maximum force = inf on atom 7370
Norm of force = inf
不止我遇到了这种问题，似乎是由于原子存在重叠引起的，可是我根据提示信息查看7370原子，我没有发现什么异常 |
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发表于 Post on 2023-12-18 11:08:19
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发表于 Post on 2023-12-18 16:56:42
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