gmx_MMPBS issue

User discussions
1

GROMACS version: 2022.4
GROMACS modification: Yes/No
I recently encountered an issue while attempting to execute a GMX_MMPBSA job on our SLURM cluster. Specifically, I installed GMX_MMPBSA locally and attempted to analyze results from molecular dynamics (MD) simulations conducted using Gromacs 2022.4.

However, upon running the job, I received the following error message:

[DEBUG ] Reading structure file
[DEBUG ] Reading file md_0_10.tpr, VERSION 2022.4 (single precision)
[DEBUG ]
[DEBUG ] -------------------------------------------------------
[DEBUG ] Program: gmx make_ndx, version 2019.6
[DEBUG ] Source file: src/gromacs/fileio/tpxio.cpp (line 2695)
[DEBUG ]
[DEBUG ] Fatal error:
[DEBUG ] reading tpx file (md_0_10.tpr) version 127 with version 116 program
[DEBUG ]
[DEBUG ] For more information and tips for troubleshooting, please check the GROMACS
[DEBUG ] website at Common Errors — GROMACS webpage https://www.gromacs.org documentation
[DEBUG ] -------------------------------------------------------
[ERROR ] MMPBSA_Error

/usr/bin/gmx make_ndx failed when querying index.ndx

Check the gmx_MMPBSA.log file to report the problem.

Could you please assist me in troubleshooting this issue? Any guidance or support you can provide would be greatly appreciated.

Thank you for your attention to this matter.

2

Do you have index file in directory?

3

yes, I have the attached index.ndx file in my directory
index.txt (2.4 MB)

4

You have two different versions of gromacs, you need to create new tpr that matches with MMPBSA tool.

5

I’m using only the gromacs 2022.4 installed on a cluster and I don’t have any other versions, but gmx_MMPBSA is installed on the local directory

6

[DEBUG ] reading tpx file (md_0_10.tpr) version 127 with version 116 program

create a tpr with version 2019.6, you can load this version from the conda environment you in which you installed the gmx_MMPBSA package.

7

Thanks a lot for your kind reply and cooperation.
I installed gmx_MMPBSA on my windows labtop and when trying to execute a job
my files (snapshot.pdb, md_0_10.tpr, index.ndx, and topol.to), I got the error message (PDBError: Coordinate shape mismatch. Probably caused by different atom counts in some of the PDB models.
Any help with that would be appreciated

8

check the tpr and xtc why do you need .pdb file? share the full command you used

9

I used this: mpirun -np 4 gmx_MMPBSA -O -i mmpbsa.in -cs md_0_10.tpr -ci index.ndx -cg 1 13 -ct snapshot.pdb
when I used xtc file, I got the same error also

10

-ct trajectory

11

got the same error with the traj.xtc. maybe the problem connected to cleaning the topology from water and ions?

12

Yes, you shoud use the whole system.