GROMACS version: 2024.1
GROMACS modification: No
Hi, hope you all are doing well. I faced an error while performing gmx_mmpbsa for my smd trajectory file. here is the problem:
it says that it can not find the atom no. 56464 in the trajectory file, while I checked: .tpr , .xtc, .gro and .ndx files for atom match.
In fact, these files are the ones from my simulation md-pull run step and they have worked properly. Now, I can not understand the problem.
However, there is one thing, for smd, I put my ligand info in the end of the .gro file (it is docking coordination result), then used pulling force for smd. This atom number is for the first atom of my ligand as well. I have .itp file of the ligand in toppar folder as well.
Can anyone please help me with this? I really appericiate you, it is kinda of forced situation.