Re: [AMBER] segmentation fault on tleap

From: Giorgos Lamprinidis <>
Date: Tue, 5 Jul 2011 18:48:03 +0300

Dan, thanks for your reply, however ambertools 1.5 is compatible with
amber10? And if I do so, I must have amber10 folder for running sander,
pmemd etc, and amber11 folder for running ambertools? or I must combine them
just after I compile them?

Dr George Lamprinidis

-----Original Message-----
From: Daniel Roe []
Sent: Tuesday, July 05, 2011 6:44 PM
To: AMBER Mailing List
Subject: Re: [AMBER] segmentation fault on tleap


The best solution may be to upgrade to the latest version of
AmberTools, 1.5 ( It contains
many improvements and fixes to almost every part of the AmberTools


On Tue, Jul 5, 2011 at 11:32 AM, Giorgos Lamprinidis
<> wrote:
> Dear Amber users,
> Some months ago i installed successfully ambertools 1.2 on a quad core
> computer running fedora 11.
> Now i have a new computer running Fedora core 15 (64bit). I tried to
> compile ambertools. I had some problems but finally i compiled AT 1.2
> without significant errors. However when i try to "source" leaprd.ff99SB
> tleap crashes giving the next error:
> [gl.localhost gl]# $AMBERHOME/exe/tleap -f leaprc.ff99SB
> -I: Adding /opt/amber10/dat/leap/prep to search path.
> -I: Adding /opt/amber10/dat/leap/lib to search path.
> -I: Adding /opt/amber10/dat/leap/parm to search path.
> -I: Adding /opt/amber10/dat/leap/cmd to search path.
> -f: Source leaprc.ff99SB.
> Welcome to LEaP!
> (no leaprc in search path)
> Sourcing: /opt/amber10/dat/leap/cmd/leaprc.ff99SB
> Log file: ./leap.log
> Loading parameters: /opt/amber10/dat/leap/parm/parm99.dat
> Reading title:
> PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
> incl.02/04/99
> Loading parameters: /opt/amber10/dat/leap/parm/frcmod.ff99SB
> Reading force field modification type file (frcmod)
> Reading title:
> Modification/update of parm99.dat (Hornak & Simmerling)
> Loading library: /opt/amber10/dat/leap/lib/all_nucleic94.lib
> /opt/amber10//exe/tleap: line 8: 29298 Segmentation fault      (core
> dumped) /opt/10/bin/teLeap -I/opt/amber10/dat/leap/prep
> -I/opt/amber10/dat/leap/lib -I/opt/amber10/dat/leap/parm
> -I/opt/amber10/dat/leap/cmd $*
> Next i tried to copy the whole "amber10" directory from the old pc to the
> new one. I still get the same segmentation fault.
> Does anyone has the same problem? How can i figure out what goes wrong?
> It may be some libraries i must install to bypass this error?
> Any help would me gvaluable.
> Yours
> Dr George Lamprinidis
> _______________________________________________
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Received on Tue Jul 05 2011 - 09:00:07 PDT
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