VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Sep 18 2008 - 22:45:03 CDT

Ah, I see. Do you sitll get the error after adding appropriate mass
lines to your topology file? You need to have each atom type that occurs
in your residue specified, and you're using type names (notably, HO)
that don't already occur in the charmm topology file you mentioned.
Peter

Nd S wrote:
> 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