From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Jun 15 2015 - 11:10:14 CDT

On Mon, Jun 15, 2015 at 11:55 AM, Sakinah Ellickson
<Ellickson.Sakinah_at_iowacityschools.org> 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!

please pay attention to this error message. this indicates that your
atom selection didn't select atoms. most likely, because you are using
characters in your residue name that have special meaning in atom
selection strings.

i suggest you first "debug" your atom selection with a VMD
representation (e.g. have one representation visualize with "Lines"
and use the selection "all" and then add a second representation with
VDW where you try out the selection that you want to use).

axel.

> 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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-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.