From: Axel Kohlmeyer (
Date: Wed Dec 11 2013 - 07:21:06 CST

On Wed, Dec 11, 2013 at 11:26 AM, Ramin Ekhteiari <> wrote:
> I generated a pdb file from my MD trajectory ( 1 step), but When I try to
> load it via other visualize programs (e.g., maestro), I face with some
> topology problem (as my pdb file is lack of any topology data), how can I
> include the connection data into pdb file ?

PDB files typically do not contain connection data (there are CONECT
records possible, but those are meant for exceptional bonds only).
typically connection (aka topology) information for MD packages is
provided in topology files e.g. .psf. or in file formats like mol2
that contain both coordinate and topology information.


> Would be grateful for any advise.
> Cheers,
> Ramin

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.