Re: Add bonds and topology file problem

From: Axel Kohlmeyer (
Date: Sun May 01 2011 - 15:52:30 CDT

On Sun, May 1, 2011 at 4:20 PM, Edroaldo Lummertz da Rocha
<> wrote:
> Hi NAMD users, when I add bonds between atoms in my model with topotools
> plugin and save the .psf file, the atom types is replaced by atom names and

can you please produce a script or sequence of commands that you
execute that demonstrates that? topotools is not supposed to and to the
best of my knowledge does not change any atom types unless you explicitly
ask for it.

> when I do a molecular dynamics I got an error related to that. For example,
> in my parameter file I have the atom type AU for gold and in my topology
> file I have atom names as A1, A2, An.  I have a psf file fo my all system
> where I have the atom names and atom types as I said before but when I add
> bonds in Tk console and save using "animate write psf test.psf" , the atom
> types in the .psf file are replaced by the atom names I got an error to
> execute a molecular dynamics. Does anybody have a suggestion?

the only explanation that would be consistent with that behavior would be
that you load a .pdb file and not the corresponding .psf file and then save
a .psf from it.


> --
> Edroaldo Lummertz da Rocha

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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