Different atoms numbers in topology and complex structure

[Axelle Thébault]

Hello,

I am facing an issue when trying to use gmx_MMPBSA, and I have been having this error 9 times out of 10 when running the program, even with different structures and MD. The error is the following:

MMPBSA_Error:

The number of atoms in the topology (2755) and the complex structure (2744) are different. Please check these files and verify that they are correct. Otherwise report the error...

Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.

I understand there seems to be a mismatch of atom numbers between the two files, but I don't understand how so. When I visualize the MD simulation on PyMOL, it seems to have been performed nicely, and I got no error in my MD log files nor during the process. As said above, I have successfully conducted gmxMMPBSA calculations with some complexes a few weeks ago, but lately for most of my complexes I have this error.

I am open to any suggestions regarding this issue! Thank you.

[mariosergi...@gmail.com]

This error is almost always due to a problem with the group selection. This causes the selected complex to have a different number of atoms than the topology. You should also consider that gmx_MMPBSA has limited support for metals and no support for structural water molecules, so if they are included in any of the selected groups, they will be removed. Please, check them and If you don't find the solution after reviewing the groups in the index.ndx, send me your files for review (only 5 frames of the trajectory).