MMPBSA——index error: list index out of range

[HariniSureshKumar]

I am facing a similar index out-of-range error when decomposing pairwise residue interactions between residues which are non-consecutive in sequence, for example, residues 12 and 14. However, it works when the sets of residues are spatially proximal. I am attaching an error message here: The command used is as follows: gmx_MMPBSA -O -i decomp.in -cs test.tpr -ci test.ndx -cg 12 14 -ct test_less.xtc -cp test.top -deo decomp/r_12-14.csv -nogui

The input file for your reference: "" &general sys_name="Protein decomp" startframe=1, endframe=10, interval=1, /

&gb igb=5, saltcon=0.150, /

&decomp idecomp=1, dec_verbose=0, print_res="within 6"

/ """" Other info:

The index groups contain one residue each. Water molecules, ligands and ions are not present. Only the protein

[marioernestovaldes]

could you please send the files you are using?

[HariniSureshKumar]

test.zip I am attaching the zipped folder containing the files. I suspect it might be one of the cut-offs but I am not entirely sure

[marioernestovaldes]

Are you trying to perform the calculation between two residues form the same unit? same protein?

[HariniSureshKumar]

Yes, it is within the same protein and same unit

[marioernestovaldes]

Unfortunately, gmx_MMPBSA requires two units that will figure as "receptor" and "ligand". Calculations for residues within the same unit is not possible...

[HariniSureshKumar]

It is quite perplexing since I am able to perform calculations when I define two consecutive residues (within the same protein) or two contiguous stretches of residues as two separate units (receptor and ligand), but not if the residues are far apart.

Is there a workaround/different module to get pairwise residue-level interactions, perhaps?

[marioernestovaldes]

That's interesting, although it is not designed to do so... it is possible to obtain pairwise residue-level interactions for regular complexes

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

[HariniSureshKumar]

I see. I was hoping to get pairwise interactions within the protein. Thank you for the prompt help though! Much appreciated