VMD-L Mailing List

From: Emily Chen (chen2041_at_umn.edu)
Date: Mon Jun 21 2010 - 14:06:19 CDT

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