VMD-L Mailing List

From: FRANCESCO TORRICELLA (francesco.torricella_at_stud.unifi.it)
Date: Thu Nov 08 2018 - 08:58:57 CST

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?