warning: The complex structure is inconsistent. The following residues are duplicates:

[Bernard Hehlen]

Hello, 

I have the warning below when I run gmx_MMPBSA with a protein A with its glycans and a protein B with its glycan. I suspect the problem arises from the fact that sugars BGLC and BMAN appear two times  with the same name in group B (they below to two separate glycans). How can I fix that, please? 

I copy my gmx_MMPBSA command line for info. 

Thank you in advance for your help.

Bernard

command lin : 

 gmx_MMPBSA -O -i mmpbsa.in -cs complex.tpr -ct all_aligned.xtc -ci index_mmpbsa.ndx -cg 3 4 -cp  topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

WARNING

[WARNING] The complex structure used is inconsistent. The following residues are duplicates:
 B:1:BGLC:, B:2:BGLC:, B:3:BMAN:, B:1:BGLC:, B:2:BGLC:, B:3:BMAN:

[mariosergi...@gmail.com]

Most of the time, this happens because the maximum length of a residue name is 4 characters in PDB format, while in the topology, it can be longer. Therefore, when truncated, the identifying characters are lost. We typically use the PDB file as the temporary export format for gromacs to perform internal analysis, checks, and other actions to ensure correspondence between the selected groups and the topology. Sadly, gromacs does not support writing mmCIF (https://gitlab.com/gromacs/gromacs/-/issues/4753), which is the most suitable format for this. As long as it's a warning, it should work without problems. If you have any problems, you can try changing the waste name to a unique four-character name.