Error while analyzing .tpr file generated using gromacs 2025.2

User discussions
1

GROMACS version:2025.2
GROMACS modification: Yes/No
The .tpr file generated by gromacs 2025.2 gave error while I am trying to analyze in ucsf chimra. I am sharing the error messages and ask for your suggestions to resolve this issue, Thank You.

using memory mapping
VERSION 2025.2
using floats
version 137, generation 28
33648 atoms
Protein in water
mol name: Protein_chain_A
3423 atoms
222 residues
mol name: CR
5 atoms
6 residues
IndexError Exception in Tk callback
Function: <function command at 0x7be006d65c08> (type: <type ‘function’>)
Module: <module ‘chimera.baseDialog’ from ‘/opt/UCSF/Chimera64-1.19/share/chimera/baseDialog.pyc’> (line: 447)
Args: ()
Traceback (innermost last):
File “/opt/UCSF/Chimera64-1.19/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py”, line 1747, in call
return apply(self.func, args)
File “/opt/UCSF/Chimera64-1.19/share/chimera/baseDialog.py”, line 449, in command
getattr(s, buttonFuncName(txt))()
File “/opt/UCSF/Chimera64-1.19/share/chimera/baseDialog.py”, line 704, in OK
self.Apply()
File “/opt/UCSF/Chimera64-1.19/share/Trajectory/EnsembleLoader.py”, line 92, in Apply
self.callback)
File “/opt/UCSF/Chimera64-1.19/share/Trajectory/formats/Gromacs/init.py”, line 68, in loadEnsemble
startFrame, endFrame, callback)
File “/opt/UCSF/Chimera64-1.19/share/Trajectory/formats/Gromacs/init.py”, line 79, in loadEnsemble
ensemble = Gromacs(topology, trajectory, startFrame, endFrame)
File “/opt/UCSF/Chimera64-1.19/share/Trajectory/formats/Gromacs/Gromacs.py”, line 26, in init
self.topology = TprTopology(topology)
File “/opt/UCSF/Chimera64-1.19/share/Trajectory/formats/Gromacs/Gromacs.py”, line 104, in init
self._readTopology(version)
File “/opt/UCSF/Chimera64-1.19/share/Trajectory/formats/Gromacs/Gromacs.py”, line 500, in _readTopology
self.resNames.append(symbols[self.xdr.unpack_uint()])
IndexError: list index out of range

IndexError: list index out of range

File “/opt/UCSF/Chimera64-1.19/share/Trajectory/formats/Gromacs/Gromacs.py”, line 500, in _readTopology
self.resNames.append(symbols[self.xdr.unpack_uint()])

See reply log for Python traceback.

2

Can Chimera read tpr files? I do not see it as supported in the list of supported file types.

3

Yes, chimera do support .tpr file you can check it in MD Simulation section in chimera tools. But this issue is not only with chimera when I had tried to calculate the protein ligand binding energy using gmxMMPBSA v1.6.3 gmx make_ndx failed when querying index.ndx. I am attaching the log file you can check.

gmx_MMPBSA.log (4.7 KB)

4

Ah that I didn’t know! Do you have other tprs that work? Usually when I have problems with external tools reading tpr files the issue is related to the GROMACS version. Have you tried recompiling it with some older version, maybe one that to you remember that worked properly.

5

Yes, till this time I have been using gromacs 2024.4 and the older versions, and those worked properly without any errors like this. I hadn’t addressed any issue during the installation of gromacs 2025.2 and after that everything worked fine except this .tpr files. So, can you please suggest something and help me out.

6

I do not think this is in any way related to the GROMACS installation. This is some problem of Chimera interfacing with the tpr. It is most likely some change in the tpr file packing that is not read correctly anymore by Chimera. I do not think there is any workaround with GROMACS 2025, I would say that your two best options are i) recompile the same tpr with an older version of GROMACS to keep the compatibility or ii) wait for a Chimera update that fixes the (un)compatibility with the newer GROMACS versions.

7

Okay thank You, I will try the suggestions and update the remarks.