VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Jan 24 2010 - 13:51:27 CST

Hi,
  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.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

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?
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078