求助使用Amber的MMPBSA.py，拓扑文件的周期性报错问题

yogurt

我的分子动力模拟是使用Gromacs跑的，体系是两条肽链的复合物，模拟结束后，我想用Amber的MMPBSA.py计算结合自由能我使用VMD把soled_complex.xtc轨迹转换为solved_complex.crd，然后用溶剂化的复合物体系的solved_complex.gro和solved_complex.top文件用parmed的python包转换生成了solved_complex.prmtop文件，然后使用ante-MMPBSA.py生成了complex.prmtop,recepter.prmtop和ligand.prmtop。然后我就按照教程运行后，提示complex.prmtop文件的周期性有问题，期间我使用了各种不同处理方式的轨迹文件（因为我觉得可能是轨迹的问题），但是始终没能解决。下面贴出报错代码。希望有知道解决方法的老师不吝赐教。


Loading and checking parameter files for compatibility...
cpptraj found! Using /home/wanghao/workhome/MD/amber18/bin/cpptraj
mmpbsa_py_energy found! Using /home/wanghao/workhome/MD/amber18/bin/mmpbsa_py_energy
Preparing trajectories for simulation...
10 frames were processed by cpptraj for use in calculation.


Running calculations on normal system...


Beginning GB calculations with /home/wanghao/workhome/MD/amber18/bin/mmpbsa_py_energy
  calculating complex contribution...
Found an invalid periodicity in the prmtop file: 1715
  File "/home/wanghao/workhome/MD/amber18/bin/MMPBSA.py", line 100, in <module>
    app.run_mmpbsa()
  File "/home/wanghao/workhome/MD/amber18/lib/python3.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/home/wanghao/workhome/MD/amber18/lib/python3.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/home/wanghao/workhome/MD/amber18/lib/python3.7/site-packages/MMPBSA_mods/calculation.py", line 157, in run
    self.prmtop))
CalcError: /home/wanghao/workhome/MD/amber18/bin/mmpbsa_py_energy failed with prmtop complex.prmtop!
Exiting. All files have been retained.

yogurt

顶一下

八月的雨季

请问解决了吗？我也遇到了同样的问题，能咨询一下吗？

紫丹渡津

我虽然没有用过，但是有gromacs工具包直接支持MMPBSA分析啊，不需要转换成amber格式：

https://github.com/RashmiKumari/g_mmpbsa

https://github.com/aspitaleri/gmxpbsa

其中第二个链接的工具稍微新一点，第一个链接只支持到gromacs 2016版本。祝好运！

yogurt

紫丹渡津 发表于 2020-12-17 05:27
我虽然没有用过，但是有gromacs工具包直接支持MMPBSA分析啊，不需要转换成amber格式：

https://github.c ...

Amber里面有MMGBSA的选项，这两个工具不能算GBSA

冷血

试试用leap重新生成top？？

UrnotNancy

请问解决了吗？我也遇到了同样的问题，能咨询一下吗？(我是Amber生成的蛋白和小分子的拓扑文件，leap和ante-mmpbsa生成拓扑文件都试过了，仍旧是上述报错）

wxx18879173572

好像是top中有原子不连续，所以top中由amber tools20中cpptraj生成的坐标会认为和mmpbsa生成的原子数不匹配。
When this structure is processed with the cpptraj (v4.25.6) version of AmberTools20, it inserts TERs after them and interprets them as independent residuals. Therefore, there is a mismatch between the number of atoms in the topology (correctly generated by gmx_MMPBSA) and the coordinates (generated with cpptraj internally during the process). However, with the cpptraj version (v5.1.0) of AmberTools21, it does not happen, apparently because they corrected the TER insertion in atoms distant from their residues, probably when there is PBC. (the reason why we initially couldn't reproduce your error)
So the solutions are as follows:
You can upgrade AmberTools and drag structural problems from your system or
You use a fully consistent system structure, with which either AmberTools20 or 21 will work correctly.