VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 22 2006 - 16:58:16 CST
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- In reply to: George M Giambasu: "autoionize "error procesing bonds""
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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
- Next message: Anuradha Mittal: "solvation"
- Previous message: John Stone: "Re: distance tween two atoms"
- In reply to: George M Giambasu: "autoionize "error procesing bonds""
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