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

[Mark Abraham]

Hi,

Unfortunately, pdb2gmx is only aware of chain ids, so you will not be able
to preserve segment id. If the atom ordering is unchanged then you don't
need the resulting PDB file, ie can use the original one. If not, then it's
straightforward to use some scripting tool to re-unite your segment id with
the output PDB.

Mark

On Wed, 13 Jan 2016 17:52 Maxim Igaev <migaev at gwdg.de> wrote:

> 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
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