Re: Problem in generating psf

From: Peter Freddolino (
Date: Thu May 31 2018 - 07:31:46 CDT

Dear Srjita,
Please make sure that the atom names in your pdb match those in the
topology file (they don't). Without that information, psfgen cannot match
the coordinates to the atoms in the topology.

On Thu, May 31, 2018 at 2:25 AM, Srijita Paul <> wrote:

> Hi,
> I have a pdb file of dodine. I have generated its topology file from
> CGENFF software. But when I am trying to regenerate pdb and psf of dodine
> using this rtf file the newly generated pdb file has all the coordiantes
> 0.00. Both the pdb and rtf file is attached here. What is the probable
> reason of this kind of problem?
> Thank you
> Srijita Paul

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