How to fit md results(.gro) to original pdb file

User discussions
1

GROMACS version: 2021.5
GROMACS modification: No
Hello,
I want to fit my final MD result fo protein-ligand complex to its original pdb file.
what i tried is
gmx trjcov -s orginal_protein.pdb -f md_reuslt.gro -o temp.gro -fit rot+trans
then i choose protein backbone for LSF and choose whole system for output.
The reulst of above is Segmentation fault (core dumped)
I think it’s due to adding ions and waters to system and adding hyrdogen to protein.
Before fitting, I used “trjconv pbc nojump” to remove pbc condition of final reuslt

So is there any way to fit final result to original PDB file?

2

I solved it myself.

Extract only ligand and protein complex with trjconv and index.ndx file
Then after fitting with original “complex.gro”, you can get fitted version of md result