MMPBSA_Error The atom 4074 in the complex index is not found in the topology file. Please check that the files are consistent..

[Soumya Lipsa Rath]

Hello,

I am trying to run MMPBSA for a protein-ligand complex. The index file has complex, protein and ligand as required. Since, I am using Charmm36, I have also given the topology file. However, it stops abruptly saying

"MMPBSA_Error The atom 4074 in the complex index is not found in the topology file. Please check that the files are consistent.."

4074 is the starting atom for the ligand molecule. Although, the topology file has both protein and ligand specified, the _temp_top.top doesn't show the ligand under the [molecules] heading.

Please help me solve this error

Thanks,

Soumya

[Mario Ernesto]

Can you please send the files you are using?

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[Soumya Lipsa Rath]

Please find the files attached

This is the command I had used

gmx_MMPBSA -O -i mmpbsa.in -cs md.tpr -ci index_ndx.ndx -cg 1 13 -ct traj_last10.xtc -cp topol.top

Thanks,

Soumya

[marioe911116]

Please, attach or send me a email with coupe of frames of the trajectory