> On Wed, Feb 08, 2012, vladanstefanovic.kg.ac.rs wrote:
>>
>> I successfully installed amber11 and ambertools1.5 on ubuntu linux, but
>> now I have a problem;
>> Each time I try to source leaprc.ff99SB console displays "segmentation
>> fault" without loading xleap;
>
> 1. Does the same thing happen with tleap?
> 2. Are you sure you are running the AmberTools 1.5 of xleap? Be sure that
> the
> output of "which xleap" points to the correct location.
> 3. Is this a 32-bit or a 64-bit version of Ubuntu?
>
> If you can't figure it out, try installing AmberTools only, into a fresh
> directory tree. We run this code on Ubuntu all the time, and it should
> not
> segfault just upon loading a leaprc file.
>
> ....dac
>
Hi David, the answers on your questions:
1. yes, the same thing happens when I start tleap, it displays:
-I: Adding /usr/local/amber11/dat/leap/prep to search path.
-I: Adding /usr/local/amber11/dat/leap/lib to search path.
-I: Adding /usr/local/amber11/dat/leap/parm to search path.
-I: Adding /usr/local/amber11/dat/leap/cmd to search path.
-s: Ignoring startup file: leaprc
-f: Source leaprc.ff99SB.
Welcome to LEaP!
Sourcing: ./leaprc.ff99SB
Log file: ./leap.log
Loading parameters: /usr/local/amber11/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
incl.02/04/99
Loading parameters: /usr/local/amber11/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading library: /usr/local/amber11/dat/leap/lib/all_nucleic94.lib
Segmentation fault
root.Vlada-AsteriX:/usr/local/amber11/exe# cd ..
root.Vlada-AsteriX:/usr/local/amber11# cd AmberTools/
root.Vlada-AsteriX:/usr/local/amber11/AmberTools# cd exe
root.Vlada-AsteriX:/usr/local/amber11/AmberTools/exe# ./xleap
-I: Adding /usr/local/amber11/dat/leap/prep to search path.
-I: Adding /usr/local/amber11/dat/leap/lib to search path.
-I: Adding /usr/local/amber11/dat/leap/parm to search path.
-I: Adding /usr/local/amber11/dat/leap/cmd to search path.
Segmentation fault
2. my xleap is in folder usr/local/amber11/AmberTools/exe
3. it is 64-bit version of ubuntu
I hope this helped finding a solution for my problem, thank you anyway.
>
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Received on Wed Feb 08 2012 - 07:30:03 PST
