VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Thu Nov 08 2018 - 11:29:36 CST

Dear Francesco,
It would help if you could post your pdb file, or at least a large enough
chunk of it to reproduce the error. Also, please clarify, does this happen
when you open the autopsf gui, or at some particular stage? If so, which
stage?
Thanks,
Peter

On Thu, Nov 8, 2018 at 11:34 AM FRANCESCO TORRICELLA <
francesco.torricella_at_stud.unifi.it> wrote:

> Hi everyone,
>
> I'm trying to prepare the psf file for a pdb. The pdb I'm using is a beta peptide that I modeled. When I try to launch autopsf I get this error:
>
> ERROR: failed at the end of the segment
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to restart.
> ERROR: failed at the end of the segment
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to restart.
> during the execution
> "segment $ segid {
> pdb $ segfile
>
> # We are aliases of the OXT C-terminal atoms on OT2 so that psfgen should guess one less atom.
> # Otherwise psf ... "
> ("psfsegments" procedure line 37)
> invoked from within
> "psfsegments $ logfileout"
> (procedure ":: autopsf :: afterchains_gui" line 66)
> 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 23)
> invoked from within
> "tk :: ButtonUp .autopsf.chains.finish"
> (command associated with the event)
>
> can someone tell me the right direction on how to solve this problem?
>
>