# Trjconv ignoring chainIDs (molblock) from TPR

**URL:** <https://gromacs.bioexcel.eu/t/trjconv-ignoring-chainids-molblock-from-tpr/8119>\
**Category:** User discussions\
**Tags:** gmx-trjconv\
**Created:** [January 23, 2024, 10:50pm UTC](https://gromacs.bioexcel.eu/t/trjconv-ignoring-chainids-molblock-from-tpr/8119 "2024-01-23T22:50:41Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![pbarletta](https://avatars.discourse-cdn.com/v4/letter/p/bc8723/32.png) [@pbarletta](https://gromacs.bioexcel.eu/u/pbarletta)\
**Post date:** [January 23, 2024, 10:50pm UTC](https://gromacs.bioexcel.eu/t/trjconv-ignoring-chainids-molblock-from-tpr/8119/1 "2024-01-23T22:50:41Z")

</div>

## 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:

```auto
[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:

```auto
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