Hi AMBER developers and users,
When I run the following leaprc in the tleap that comes with Amber14, the
program fails in a segfault:
set default PBradii mbondi3
source leaprc.ff14SBonlysc
source leaprc.gaff
mol_0 = sequence { NMET THR HIE GLN THR HIE ALA TYR HIE MET VAL ASN PRO SER
PRO TRP PRO LEU THR GLY ALA LEU SER ALA LEU LEU MET THR SER GLY LEU THR MET
TRP PHE HIE PHE ASN SER MET THR LEU LEU MET ILE GLY LEU THR THR ASN MET LEU
THR MET TYR GLN TRP TRP ARG ASP VAL ILE ARG GLU SER THR PHE GLN GLY HIE HIE
THR PRO ALA VAL GLN LYS GLY LEU ARG TYR GLY MET ILE LEU PHE ILE ILE SER GLU
VAL LEU PHE PHE THR GLY PHE PHE TRP ALA PHE TYR HIE SER SER LEU ALA PRO THR
PRO GLU LEU GLY GLY CYS TRP PRO PRO THR GLY ILE HIE PRO LEU ASN PRO LEU GLU
VAL PRO LEU LEU ASN THR SER VAL LEU LEU ALA SER GLY VAL SER ILE THR TRP ALA
HIE HIE SER LEU MET GLU GLY ASP ARG LYS HIE MET LEU GLN ALA LEU PHE ILE THR
ILE THR LEU GLY VAL TYR PHE THR LEU LEU GLN ALA SER GLU TYR TYR GLU ALA PRO
PHE THR ILE SER ASP GLY VAL TYR GLY SER THR PHE PHE VAL ALA THR GLY PHE HIE
GLY LEU HIE VAL ILE ILE GLY SER THR PHE LEU ILE VAL CYS PHE PHE ARG GLN LEU
LYS PHE HIE PHE THR SER ASN HIE HIE PHE GLY PHE GLU ALA GLY ALA TRP TYR TRP
HIE PHE VAL ASP VAL VAL TRP LEU PHE LEU TYR VAL SER ILE TYR TRP TRP GLY
CSER }
translate mol_0 { 0.0 0.0 0.0 }
sys = combine { mol_0 }
check sys
saveAmberParm sys system.top system.mdcrd
quit
The output says:
ERROR: syntax error
Segmentation fault (core dumped)
If I enter the commands one by one, the segfault occurs on the "sequence"
command.
If I change the sequence, but keep it the same length, the error still
occurs. If I shorten the sequence, the segfault does not occur. I can even
use a long sequence of alanines and the segfault still happens.
This makes me think that there is a memory overflow or something with
longer entries to the "sequence" command in the tleap code.
Best,
-Lane
--
Lane Votapka Ph.D.
Postdoctoral Associate, Dill Laboratory 115G
Laufer Center for Physical and Quantitative Biology
Stony Brook University
Stony Brook, NY 11794
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Received on Wed Sep 21 2016 - 14:00:03 PDT
