GROMACS version:2023.2
GROMACS modification: Yes/No
Hi, I am performing a MMPBSA calculation on a biological simulation system, which is a steered molecular dynamics simulation of molecule transport through a nanotube. When I perform pb and decomposition via gmx_mmpbsa, I get this error: “The atom 59465 in the complex index is not found in the topology file. Please check that the files are consistent.”
While, the files are all the original ones that I used for MD and SMD simulations, I cannot get the problem… all topology files are present in the directory as well.
I performed pb calculation alone, and I did not face this error…
BTW, the input file is like this:
Decomposition namelist variables
&decomposition
idecomp = 4 # Which type of decomposition analysis to do
dec_verbose = 3 # Control energy terms are printed to the output
print_res = “within 6” # Which residues to print decomposition data for
csv_format = 1 # Write decomposition data in CSV format