VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sun Jan 28 2007 - 00:38:29 CST

Hi Stanley,
paratool shouldn't be throwing an error under these circumstances --
I'll get together with the paratool developer and see if it's an issue
with having only one atom in your selection. Can I ask what version
number of VMD you are running?

In your case, zinc is present in standard topology files--you're
probably just suffering from it having the wrong residue name. The
standard topology file used by autopsf expects zinc to have the residue
name ZN2, and atom name ZN. Newer builds of VMD will also include
automatic aliasing to recognize ZN as a zinc ion, but that may not be
present in your version, so you will need to change the name manually.
If you change the residue name of your zinc, or change your topology
file, everything should work fine.

Let me know if any of this doesn't make sense.

Peter

Stanley, Yemin Shi wrote:
> Hi,
> I got a error message when generate psf from pdb. Could anybody kindly
> pls help?
>
> (WinVMD, Autopsf)
> The step outline is:
> 1) Load the molecule
> 2) Extentions->modelling->automatic psf builder
> 3) all parameter are set to default in the auto psf dialog box.
>
> Once I click the "I'm feeling lucky" button, it comes out the
> following messeger:
>
> ==================================================
> Autopsf has detected on unparameterized components:
> Don't worry, there are several things you can do:
> 1) Load additional topology file that contains missing information and
> rerun psfgen.
> 2) Delete the component from your system and rerun psfgen.
> 3) Parameterize the unknown component using Paratool.
> ----------------------------------------
> Zn 1 Atoms ZINC ION
> ----------------------------------------
>
> Once I click the parameterize button, it comes out the following error
> message:
> -------------------------------
> atomsel : setbondorderss: Need one bond order list for each selected atom
> atomsel : setbondorderss: Need one bond order list for each selected atom
> while executing
> "$atom0 setbondorders [list $bondorder0]"
> (procedure "import_bondorders_from_topology" line 84)
> invoked from within
> "import_bondorders_from_topology $molidparent"
> (procedure "::Paratool::paratool" line 103)
> invoked from within
> "::Paratool::paratool -top $topfiles -parentid $tmpmolid -unparsel
> $sel -basemol ${basename}_${resname}_${i}.xbgf -extrabonds $extrabonds"
> (in namespace inscope "::autopsf" script line 20)
> invoked from within
> "::namespace inscope ::autopsf {
> variable unparsel
> set i [.fchooser.frag.topo.list.list curselection]
> set frag [lindex $unparsel $i]
> ..."
> invoked from within
> ".fchooser.frag.topo.buttons.add invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 24)
> invoked from within
> "tk::ButtonUp .fchooser.frag.topo.buttons.add
> "
> (command bound to event)
> -------------------------------
> Thanks for help
>
> Rgds
> Stanley