No values in energy_MM.xvg despite no overlapping residues in Index file

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adi...@gmail.com

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Nov 28, 2020, 3:35:21 AM11/28/20
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Dear Users,

I have done a 300ns simulation of a protein_A-protein_B in complex with a bound small molecule and when I am calculating the binding free energy between protein_A with small molecule, and protein_B with small molecule separately, using the one step command for e.g. "g_mmpbsa -f removepbc.xtc -s protein.tpr -n index.ndx -i ../pbsa.mdp -pdie 2 -pbsa -decomp", it generated all the required output files. However, in the energy_MM.xvg file, it doesn't print any values (shows only -nan). I visualized the trajectory in Chimera just to check if it is OK and the entire trajectory looks fine.

FYI, I have also checked the index file and can confirm that the two groups in the index file does not have overlapped residues (i.e. group 1 has 1-703 residues and group 2 has 708-887 residues). Still, I am not able to understand where the problem is.  It would very helpful if any expert can help me in resolving this issue.

I look forward to the reply !

Thanks and regards
Aditya

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