From: Nd S (navdeep79_at_gmail.com)
Date: Thu Sep 18 2008 - 18:55:28 CDT

Hi all

I am trying to generate psf files using auto psfgen, for ethyl alcohol, by
defining the residue. I am getting the following error:

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 have defined the residue as:

Resi ETAL 0.00 !Ethyl Alcohol, Navdeep
Group
 Atom C1 CTL3 -0.27 !
 Atom H11 HAL3 0.09 !
 Atom H12 HAL3 0.09 ! H11 O1--HO1
 Atom H13 HAL3 0.09 ! \ /
Group ! H12--C1-C2--H21
 Atom C2 CTL2 0.05 ! / \
 Atom O1 OH1 -0.66 ! H13 H22
 Atom H21 HAL2 0.09 !
 Atom H22 HAL2 0.09 !
 Atom HO1 HO 0.43 !
Bond C1 H11 C1 H12 C1 H13
Bond C1 C2
Bond C2 O1
Bond C2 H21 C2 H22
Bond O1 HO1
IC O1 C2 C1 H11 0.00 0.00 -60.0 0.0 0.0
IC H11 C1 C2 H22 0.00 0.00 60.0 0.0 0.0
IC H11 C1 C2 H21 0.00 0.00 180.0 0.0 0.0
IC O1 C2 C1 H12 0.00 0.00 180.0 0.0 0.0
IC H13 C1 C2 H21 0.00 0.00 -60.0 0.0 0.0
IC C1 C2 O1 HO1 0.00 0.00 -60.0 0.0 0.0
IC HO1 O1 C2 H21 0.00 0.00 60.0 0.0 0.0
patc firs none last none

and the pdb file I am using is:

CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
ATOM 1 C1 ETALX 1 -0.833 -0.385 -0.123 1.00 0.00
C
ATOM 2 C2 ETALX 1 0.550 0.243 -0.380 1.00 0.00
C
ATOM 3 O1 ETALX 1 1.408 0.092 0.854 1.00 0.00
O
ATOM 4 H11 ETALX 1 -0.708 -1.492 0.120 1.00 0.00
H
ATOM 5 H12 ETALX 1 -1.481 -0.271 -1.054 1.00 0.00
H
ATOM 6 H13 ETALX 1 -1.332 0.143 0.755 1.00 0.00
H
ATOM 7 H21 ETALX 1 0.425 1.350 -0.623 1.00 0.00
H
ATOM 8 H22 ETALX 1 1.050 -0.285 -1.258 1.00 0.00
H
ATOM 9 HO1 ETALX 1 0.920 0.605 1.708 1.00 0.00
H
END

Thanks

Navdeep