Re: Building molecule from topology file

From: Peter Freddolino (
Date: Sat Aug 26 2006 - 10:44:23 CDT

Hi Javier,
the topology file specifies connectivities, force field types, and
charges, as well as how to add in the coordinates of missing atoms, but
you still need some starting set of coordinates to create a pdb. If you
don't have them available you can use the VMD molefacture plugin or an
external program (like MOE) to build the molecule you need.

Lechuga, Javier wrote:
> Hello,
> Do you know if there is a way to build a molecule from its topology file?. Therefore you could get the "pdb" and "psf" file.
> Thank you,
> Javier

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