VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Jun 21 2010 - 18:42:33 CDT

Hi Emily,
The link that you gave is not to a tutorial, just some documentation on
the cgtools plugin, so it is not clear exactly what you have done. If
you can describe step by step what you did (starting from what pdb code
you're using), we may be able to help. Giving a snippet of the pdb file
that you're using as input to autopsf would also be useful, as would
more complete output from autopsf.
Best,
Peter

On 06/21/2010 03:06 PM, Emily Chen wrote:
> To anyone willing to help,
>
> I am learning how to make coarse-grain models.
> I have generated coarse-grain pdbs using the CG Builder tool. I am
> trying to create coarse-grain psf files using AutoPSF. I am using the
> default topology file: "rbcg-2007.top." I am following the directions
> in this tutorial: http://www.ks.uiuc.edu/Research/vmd/plugins/cgtools/
>
> However, the "Create chains" step, I am consistently getting an error:
>
> /MOLECULE/ DESTROYED BY FATAL ERROR! /Use resetpsf to start over/.
>
> or
>
> MOLECULE MISSING! Use resetpsf to start over.
>
> MOLECULE MISSING! Use resetpsf to start over.
> while executing
> "topology ${basename}-temp.top"
> (procedure "::autopsf::afterchains_gui" line 22)
> invoked from within
> "::autopsf::afterchains_gui"
> invoked from within
> ".autopsf.chains.finish invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 24)
> invoked from within
> "tk::ButtonUp .autopsf.chains.finish"
> (command bound to event)
>
> I have tried this for ubiquitin and Ikba, and both of them stop
> working at that point. Could you give me some direction about what to
> do, point me to a tutorial, or list some molecules that would work?
> Thank you so much!
>
> Sincerely,
> Emily Chen
>