The Error about "gmx make_ndx failed when querying index.ndx "

[오형철]

I rigorously searched about this topic, but I can't find the answer..

I just tried to do gmx_MMPBSA in protein-ligand (1 drug).

I Prepared the input files such as xtc, gro files using Charmm_gui. 

I also newly make index.ndx file using this command:  

gmx make_ndx -f xxx.pdb -o index.ndx

after that, I could find a index of protein and drug

The protein group number was 1 and ligand number was 13 

thus, I did mmPBSA with this command:

gmx_MMPBSA -O -i mmpbsa.in -cs step5_1.tpr -ci index.ndx -cg 1 13 -ct step5_1.xtc -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

But, after that I got errors like this. 

MMPBSA_Error:

/home/xxx/.miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx make_ndx failed when querying index.ndx

Could you help me to solve this problem?

the log file, I attatched.

Thank you for your help

[marioe911116]

The thing is that the GROMACS installed in the environment is 2022.4 while the one used to generate the tpr file is 2023.1. Please, update GROMACS accordingly and it should work

conda install -c conda-forge gromacs==2023.1