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