GROMACS version: 2022.3
GROMACS modification: No
Dear users and developers of GROMACS! I want to report a small problem that I had recently with recording the trajectory of my simulation.
I have GROMACS 2022 on my laptop and on a computing server. On the personal computer I prepare the files for launch and do all the processing of the results, and on the server I just make grompp preprocessing and modeling. This time I modeled a protein with a modified phosphotyrosine residue in the CHARMM force field. At laptop, I added this residue to my residuetypes.dat file, but not on the server, I forgot to do this. I prepared the system for simulation, uploaded the files to the server and ran grompp and then mdrun. Everything started without any errors. In the mdp file, it was instructed to save the xtc trajectory only for the protein with compressed-x-grps option. Upon completion of the simulation, I found that my modified residue was not recognized by GROMACS as a protein (which is logical as I forgot to add it to the list of protein residues on the server) and the trajectory for it was not recorded. Accordingly, errors occurred when i was trying to analyze the trajectory and calculate parameters like RMSD for it. I tried to make gmx convert-tpr and the phosphotyrosine residue in it was surprisingly interpreted as a protein, so I firstly had to make an index file for the protein, secondly make a new tpr using index file, and only then process the trajectory. In the end, everything worked, but I will most likely redo the modeling anyway.
I’m posting here in case anyone has the same problem. I was frustrated that this error cannot be caught in advance, before the simulation is completed, and then, accordingly, cannot be corrected. Be careful with your modified residues :)
Best regards,
Anna