GROMACS version: 2023.2
GROMACS modification: No
I’m running trjconv with a .tpr file and a .gro file of a system composed of a protein monomer (chainID A), a metal ion (chainID B) and another monomer (chainID C). There’s also some water and ions.
The thing is that the output PDB does not assign a chainID to the ion and gives the chainID B to the second monomer, when it should be C. That is, instead of reading the chainIDs from the .tpr file, it generates them by itself.
I’m going around this by using MDAnalysis but I was wondering if this is expected behaviour.
Thanks for any info.
Some extra details:
I built the TPR using a topology with the following chains/molecules:
[ molecules ]
; Compound #mols
A 1
B 1
C 1
NA 83
CL 87
WAT 28348
Molecule ‘B’ is just a manganese atom.
I can also check that these molecules are preserved as molblock on the .tpr, by reading the file with MDAnalysis:
0,seg_0_A
1,seg_1_B
2,seg_2_C
3,seg_3_NA
4,seg_4_CL
5,seg_5_WAT
So I’m sure this is due to trjconv.
I’m sorry I can’t share any files