gmx_MMPBSA does not support water/ions molecules

Seetha Rama Sastry Gudimetla

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Aug 5, 2026, 2:33:53 AM (12 days ago) Aug 5

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Hi, I am trying to run a ion binding protein-ligand complex where the ion which stabilizes the complex is Na+. When i try to run the gmx_MMPBSA it is throwing the error. I have tried renaming the ion but it is not working.

gmx_MMPBSA.log

marioe911116

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Aug 5, 2026, 3:14:16 AM (12 days ago) Aug 5

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Did you also rename the ion in the topology and teh structure with a different name, let's say "NAI"?

Seetha Rama Sastry Gudimetla

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Aug 5, 2026, 3:15:44 AM (12 days ago) Aug 5

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yes

marioe911116

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Aug 5, 2026, 3:17:48 AM (12 days ago) Aug 5

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Can you share teh files you are using? Only 5 frames in the trajectory

Seetha Rama Sastry Gudimetla

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Aug 5, 2026, 4:52:05 AM (12 days ago) Aug 5

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files.tar.xz

Seetha Rama Sastry Gudimetla

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Aug 5, 2026, 4:57:33 AM (12 days ago) Aug 5

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On Wednesday, August 5, 2026 at 2:22:05 PM UTC+5:30 Seetha Rama Sastry Gudimetla wrote:

10frames.xtc

marioe911116

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Aug 5, 2026, 1:00:07 PM (12 days ago) Aug 5

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I need these files:

-mmpbsa_t6p.in

-topology_clean_2.pdb

-clean_groups_2.ndx

-the topology file as well as any additional folders that are not included in GROMACS

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