[gmx-users] pdb2gmx, chain and segment names in the output pdb

[Maxim Igaev]

Dear Gromacs users,

I have a large molecular complex consisting of many identical monomers.
I constructed a pdb file for it using VMD and assigned each monomer
a segment name (A0, A1, A2 etc.). The chain name was however always
the same - A. Then I created the topology for it using pdb2gmx.

In the output pdb file, however, all segment names have disappeared
and the chain names have changed - instead of A for each monomer, I
now have A, B, C, D etc for the first ~20 monomers and then simply
nothing for the rest of the monomers.

Is there a way to make pdb2gmx preserve segment/chain names while
creating a topology file?

I need my initial naming since I want to postprocess my trajectories
in VMD again.

Thanks a lot in advance!

Cheers,
Maxim