Hi-
I'd like to report a problem I've been having with xleap. It crashes with
a Segmentation fault. The error message is
"/home/mickey/amber12/bin/xleap: line 19: 79488 Segmentation fault
$AMBERHOME/bin/xaLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib
-I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*"
The frustrating thing is that the crash is not completely reproducible.
I'm running AmberTools12, under cygwin, on Windows 7. I start xleap with:
xleap -f leap.L.in
The leap.L.in file is simple:
source leaprc.ff99SB
x = loadpdb monomer.1.pdb
y = loadpdb monomer.2.pdb
The crash seems to happen after I use the remove command:
remove x x.2
And then I try to add amino acids to the N-terminus:
set x head x.3.N
part3 = sequence { NSER LEU x }
I've attached the log file from when xleap crashed (leap.log.2), as well as
when I was able to quit successfully (leap.log.3), as well as both .pdb
files described above.
Before the last crash (described in leap.log.2), there was a message in
xleap that might be a clue to what is happening:
Error: Atom has force field coordination 0
but only 1 bonded neighbors.
The cause may be an incorrect atom type, and
the effect may be a crash very soon.
A similar message can be seen at the end of leap.log.2. That message did
not appear in xleap, as the program just crashed.
--
With best regards,
--Mickey Richards
Department of Chemistry
University of Alberta
email: mickey18385.gmail.com
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Received on Thu Dec 04 2014 - 15:30:03 PST
