From: Josh Vermaas (
Date: Mon Jun 15 2015 - 11:28:14 CDT

Hi Sakinah,

Well, for just the ion, I would actually default to making it manually,
as you may be deviating too far from what autopsf was meant to do, which
is deal with making psfs for proteins and nucleic acids. In principle,
this would be the basic script:

package require psfgen ; #Tell VMD to load the package for psf generation
resetpsf ; #Clear out psfgen memory. Lets you rerun the script if you
modify it to fix an error

segment UION { ; #Create a segment. This makes more sense for
macromolecules than it does for ions
     first none; last none; #Don't apply patches to the end of the segment.
     residue 1 UO2 ; #UO2 needs to match the residue name in the
topology file. If it doesn't, there needs to be an alias command somewhere.
coordpdb coordinates.pdb UION ;#Load the coordinates from
coordinates.pdb into segment UION. Note that the atom names in the pdb
need to match what is defined in the topology file for this to work.

#These two lines are optional in your case, but in general save you from
missing hydrogens in the pdb
regenerate angles dihedrals

#Now write it out.
writepsf new.psf
writepdb new.pdb

For combining it with the protein part, I'd definitely look at the
topotools documentation and script it, as it has a more general use than
the merge command found in the extensions tab.

-Josh Vermaas

On 6/15/15 10:55 AM, Sakinah Ellickson wrote:
> Hello,
> I am relatively new to vmd, and have been trying to create a psf file for a project that involves uranyl ion: (UO2)2+.
> I have a pdb file for a molecule made of standard C, N, Os, and the uranyl complex. I have separated the (UO2)2+ into its own pdb file, and am hoping to create two separate psf files for the substances, then merge them later. I want to use NAMD to simulate water surrounding this molecule.
> I have created a topology file and parameter file for (UO2)2+, but every time I use Auto PSF Builder with my topology and pdb file loaded, it gives me the following error message:
> Need to have at least one atom in your selection!
> Need to have at least one atom in your selection!
> while executing
> "error "Need to have at least one atom in your selection!""
> (procedure "write_selection_tempfiles" line 34)
> invoked from within
> "write_selection_tempfiles $currentMol"
> (procedure "psfmain" line 15)
> invoked from within
> "psfmain"
> (procedure "::autopsf::runpsfgen" line 35)
> invoked from within
> "::autopsf::runpsfgen"
> invoked from within
> ".autopsf.gobutton invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 24)
> invoked from within
> "tk::ButtonUp .autopsf.gobutton"
> (command bound to event)
> I know uranium is not a "typical" atom to work with. Any suggestions or possible instructions on how to manually create my psf file?
> Thanks,
> Sakinah
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