Fatal error:
Step 0: The total potential energy is 2.80133e+15, which is extremely high.
The LJ and electrostatic contributions to the energy are 2.80133e+15 and
-63659.1, respectively. A very high potential energy can be caused by
overlapping interactions in bonded interactions or very large coordinate
values. Usually this is caused by a badly- or non-equilibrated initial
configuration, incorrect interactions or parameters in the topology.
我以为是能量最小化没有弄好，于是又进行了一次能量最小化，还是会报错。然后我去用vmd查看了一下输入结构，没发现重叠什么的。难不成是因为强行把sobtop弄出来的信息放到charmm力场中去造成的？想请教一下怎么才能解决这个报错问题。因为传输文件大小原因，上传初始文件
(, 下载次数 Times of downloads: 1)
上传 Uploaded
点击下载Click to download
。同时压缩后上传能量最小化后的gro文件
(, 下载次数 Times of downloads: 1)
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
