Trjconv not writing chain identifiers anymore (since ca. v2019)

User discussions
1

GROMACS version: 2023.1
GROMACS modification: Yes/No (required!)

Hi guys,

this question is addressing the Gromacs developers. Gromacs v2018.7 as the last version I’m aware of was able to write chain identifiers into a PDB file extracted from an XTC trajectory and using as topology (with -s) PDB files containing the corresponding chain names.

For inexplicable reasons, this feature was (accidentally or intentionally) removed, I think somewhere around v2019.x, and has still not been “fixed” (currently v2023.1). Is there any hope that Gromacs trjconv will soon regain the ability to output chain identifiers in PDB files? Trying to keep v2018.7 alive starts making things complicated.

Many thanks & best wishes
Vedat (one of your biggest fans since decades ;)

2

Is it only trjconv or also other tools like editconf?

3

editconf writes chain identifiers (fed with the same pdb file as passed to trjconv via -s and -f)

4

I uploaded a fix for release-2023:

Thanks for reporting this.

1 Like
5

Many thanks for fixing this!