VMD-L Mailing List

From: Ronald Salesky (rsalesky_at_unm.edu)
Date: Sun Jan 24 2010 - 12:29:12 CST

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?