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

[Alexey Shvetsov]

Maxim Igaev писал 13-01-2016 19:51:
> 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.

This should be fixed GROMACS master branch. It will not preserve segid, 
but it will add chain ids for all chains (up to 62 chains).

> 
> 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

-- 
Best Regards,
Alexey 'Alexxy' Shvetsov, PhD
Department of Molecular and Radiation Biophysics
FSBI Petersburg Nuclear Physics Institute, NRC Kurchatov Institute,
Leningrad region, Gatchina, Russia
mailto:alexxyum at gmail.com
mailto:alexxy at omrb.pnpi.spb.ru