VMD-L Mailing List

From: George M Giambasu (giambasu_at_GMAIL.COM)
Date: Mon Mar 20 2006 - 16:50:28 CST

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)