From: John Stone (
Date: Sun Jan 24 2010 - 13:51:27 CST

  I get the same error you're getting when I try running autopsf
on your structure. If I use "nucleic acid" for the selection checkbox,
then I don't get any program errors, but I get a bizarre bonding pattern
that's clearly not right. I'm CCing the authors of autopsf in case they
have any suggestions that may help you solve your problem.

  John Stone

On Sun, Jan 24, 2010 at 12:29:12PM -0600, Ronald Salesky wrote:
> Hello fellow VMD users,
> I am attempting to generate a psf file using the Autopsf
> plugin utility from a loaded .pdb molecule. The molecule
> is displayed beautifully in the VMD viewer and 129 atoms
> are listed in VMD main as the number of atoms, yet autopsf
> gives the error, "Need to have at least one atom in your
> selection!". Does anyone have a suggestion? I've used this
> plugin before with other .pdb files w/o encountering this
> error (and not doing anything special other than launching
> autopsf and pressing "I'm feeling lucky".)
> I have attached the .pdb in question as background. Please
> note that this .pdb represents a ssDNA strand AGCT which
> was generated w/ Tinker's nucleic and the .pdb generated
> from the VegaZZ program by opening the Tinker .xyz file
> and outputting the .pdb file.
> Much thanks in advance,
> Ron
> PS: Additionally, other than the psfgen user's manual, can
> anyone point me to a good tutorial on psfgen and a format
> definition for .psf files?

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