MoleculeError("Cannot exclude an atom from itself!

[Riddhi Sharma]

Hello,

This is the command I am using .

" gmx_MMPBSA -O -i mmpbsa.in -cs traj_dump_133.pdb -ct md_0_10_center.xtc -ci index.ndx -cg 1 13 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv"

error

    raise MoleculeError("Cannot exclude an atom from itself! "
MoleculeError: Cannot exclude an atom from itself! Atoms are: <Atom Cl1 [0]; In UNK 0> <Atom Cl1 [0]; In UNK 0>
Exiting. All files have been retained.

I ran the last command mentioned in the log separately and it gave no error.

Any help would be appreciated.

Thanks

[marioe911116]

Could you please send the files you are using?

[Riddhi Sharma]

Hi 

PFA the necessary files.

[Riddhi Sharma]

I think the cause of error is the presence of Lone pairs in my complex

[Riddhi Sharma]

I followed this tutorial and error has been resolved.

https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/examples/Protein_ligand_LPH_atoms_CHARMMff/