VMD-L Mailing List
From: Nd S (navdeep79_at_gmail.com)
Date: Thu Sep 18 2008 - 22:30:05 CDT
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Hi Peter
Actually the error I mentioned occurs at the end and the pdb and the psf
files are not generated.
So to explain it all, I have "Alcohol_autopsf-temp.pdb.",
"Alcohol_autopsf-temp.xbgf", "Alcohol_autopsf-temp.top" and a log file in my
directory (apart from the input files) , the following messages at the
console,
info) Finished with coordinate file /home/Alcohol.pdb.
Info) Opened coordinate file Alcohol_autopsf-temp.pdb for writing.
Info) Opened coordinate file Alcohol_autopsf-temp.xbgf for writing.
Info) Finished with coordinate file Alcohol_autopsf-temp.pdb.
Info) Finished with coordinate file Alcohol_autopsf-temp.xbgf.
The following pop-up error message appears before the generation of the
files:
ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
while executing
"segment $segid {
pdb $segfile
# We alias the C-terminal OXT atoms to OT2 so that psfgen has to guess
one atom less.
# Otherwise psf..."
(procedure "psfsegments" line 29)
invoked from within
"psfsegments $logfileout"
(procedure "::autopsf::afterchains_gui" line 50)
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 22)
invoked from within
"tk::ButtonUp .autopsf.chains.finish
"
(command bound to event)
I hope I am able to explain.
Thanks
Navdeep
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