VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 22 2006 - 16:58:16 CST

Hi,
  What platform are you running VMD on?
We may want to see the files you're using as well, but I'll let you know
about that later.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Mar 20, 2006 at 04:50:28PM -0600, George M Giambasu wrote:
>
>
> Hi,
>
> I am trying to use autoionize module in vmd 1.8.4b11, but I get this
> kind of error after reading the pdb/psf file:
>
> "Error processing bonds"
>
> from the graphical interface I get (see bottom). The xplor psf file was
> produced with charmm and my system consists of two RNA strands, water,
> and a modified residue (new atom types, etc..).
>
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
>
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
> while executing
> "readpsf $psffile"
> (procedure "autoionize_core" line 54)
> invoked from within
> "autoionize_core -psf
> /usr/people/giambasu/rybo/simulation/hdv_str/hdvr_wat/hdvr_mg_w_xplor_large.psf
> -pdb /usr/people/giambasu/rybo/simulation/hdv_str..."
> ("eval" body line 1)
> invoked from within
> "eval autoionize_core $args "
> invoked from within
> "if $errflag { error $errMsg $savedInfo $savedCode }"
> (procedure "autoionize" line 8)
> invoked from within
> "autoionize -psf
> /usr/people/giambasu/rybo/simulation/hdv_str/hdvr_wat/hdvr_mg_w_xplor_large.psf
> -pdb /usr/people/giambasu/rybo/simulation/hdv_str/hdvr..."
> ("eval" body line 1)
> invoked from within
> "eval autoionize $command_line"
> (procedure "::Autoi::run_autoi" line 70)
> invoked from within
> "::Autoi::run_autoi"
> invoked from within
> ".autoigui.autoi invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 22)
> invoked from within
> "tk::ButtonUp .autoigui.autoi
> "
> (command bound to event)
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078