On Mon, Apr 27, 2015, MOHD HOMAIDUR RAHMAN wrote:
> >
> > I am trying to run the tleap in AmberTool 14.25, but I am getting
> > segmentation fault error. After that I updated my amber14 and I got no new
> > update is available for amber 14. given below
> >
> > The segmented error given below, the value of segmentation error are
> > changing every time when I am running the command.
> > [rahman.localhost leap]$ tleap -s -f leap.in
> > -I: Adding /home/rahman/sware/ambertool14/amber14/dat/leap/prep to search
> > path.
> > -I: Adding /home/rahman/sware/ambertool14/amber14/dat/leap/lib to search
> > path.
> > -I: Adding /home/rahman/sware/ambertool14/amber14/dat/leap/parm to search
> > path.
> > -I: Adding /home/rahman/sware/ambertool14/amber14/dat/leap/cmd to search
> > path.
> > -s: Ignoring startup file: leaprc
> > -f: Source leap.in.
> >
> > Welcome to LEaP!
> > Sourcing: ./leap.in
> > Loading parameters:
> > /home/rahman/sware/ambertool14/amber14/dat/leap/parm/frcmod.spce
> > Reading force field modification type file (frcmod)
> > Reading title:
> > This is the additional/replacement parameter set for SPC/E water
> > */home/rahman/sware/ambertool14/amber14/bin/tleap: line 17: 7255
> > Segmentation fault * (core dumped) $AMBERHOME/bin/teLeap
This is a serious error, but one that I cannot reproduce. It has nothing to
do with your pdb file, since the error happens before that.
Your leap.in file (from Google drive) starts with this line:
source leaprc.ff99bsc0
This won't work, since the file you are referencing doesn't exist; (it is in
the "oldff" subdirectory, as an obsolete force field.) But the output above
doesn't contain any error message like "Could not open file leaprc.ff99bsc0:
not found". So I'm concerned that the leap.in file you posted is not the one
you were actually using.
First, be sure that tleap passes the test suite. Second, try to make a
minimal example with the smallest possible leap.in file. I'd suggest not
using the "-f" flag to tleap: just type in the commands by hand at the command
prompt, and see exactly when the error occurs. You may need to reinstall
Amber, to be sure that you don't somehow have a corrupted file.
...dac
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Received on Mon Apr 27 2015 - 05:30:03 PDT
