[Bug-gmx_MMPBSA]: gmx_MMPBSA does not support water/ions molecules in any structure, but we found 2 molecules in the complex

[yyf2626]

Bug summary

[gmx_MMPBSA does not support water/ions molecules in any structure, but we found 2 molecules in the complex] I want to calculate the binding free energy between a metalloprotein and a ligand, but I keep encountering the above error, and I can't resolve it. I request your help, and I greatly appreciate your assistance (the serial numbers of the sodium ions are 8871 and 8872, and I have included them in the 'protein' section of the index.ndx file). All the files are in mmpbsa.zip

Terminal output

gmx_MMPBSA does not support water/ions molecules in any structure, but we found 2 molecules in the complex.

gmx_MMPBSA.log

mmpbsa.zip

Operating system

Ubuntu

gmx_MMPBSA Version

1.6.3

Python version

3.10.13

Installation

conda AmberTools + conda

[marioernestovaldes]

Sodium is typically used along CL in MD as ions. If are interested in keeping certain sodium ions in the system, you should rename those in the input structure and topology files (something like NAI for example), so gmx_MMPBSA doesn't detect them as regular ions.

[yyf2626]

钠通常在 MD 中与 CL 一起作为离子使用。如果有兴趣在系统中保留某些钠离子，您应该在输入结构和拓扑文件（例如 NAI）中重命名它们，这样gmx_MMPBSA就不会将它们检测为常规离子。

Thank you for your response. I'll give it a try.

[yyf2626]

钠通常在 MD 中与 CL 一起作为离子使用。如果有兴趣在系统中保留某些钠离子，您应该在输入结构和拓扑文件（例如 NAI）中重命名它们，这样gmx_MMPBSA就不会将它们检测为常规离子。 I followed your method and modified the structure file and topology file, but now I am getting this error... [The number of atoms in the topology (8984) and the complex structure (8852) are different. Please check these files and verify that they are correct. Otherwise report the error...] mmpbsa.zip