Hello Rebecca,
There were numerous memory overlap issues with tleap when AmberTools 1.4 was
first released that kind of lay dormant for a long time. Mengjuei fixed
these a while ago and created a bug fix that you need to apply. See
http://ambermd.org/bugfixes.html and navigate to AmberTools 1.4 and download
bugfix.all, apply it, and try again.
Moreover, that post on somewhereville.com is fairly outdated and many
instructions have changed. The link
http://ambermd.org/ubuntu.html tells
you which packages you have to install from aptitude in order to install
Amber. After that, you can just follow the instructions in the manual to
compile AmberTools-1.4 (don't forget to apply bug fixes first).
Hope this helps,
Jason
2010/9/2 Rebeca García Fandiño <regafan.hotmail.com>
>
> Hello,
> I am trying to install Ambertools in my machine (2.6.32-24-generic
> #42-Ubuntu SMP Fri Aug 20 14:21:58 UTC 2010 x86_64 GNU/Linux ), and I
> followed the instructions in the Manual and
> http://www.somewhereville.com/?p=345.
>
> When I open tleap, it seems that everything had gone OK, however, when I
> source the leaprc.ff99SB I get a segmentation fault error when it tries to
> load the libraries:
>
> user1.regafan:/opt/amber11/exe$ ./tleap
> -I: Adding /opt/amber11/dat/leap/prep to search path.
> -I: Adding /opt/amber11/dat/leap/lib to search path.
> -I: Adding /opt/amber11/dat/leap/parm to search path.
> -I: Adding /opt/amber11/dat/leap/cmd to search path.
>
> Welcome to LEaP!
> (no leaprc in search path)
> > source leaprc.ff99SB
> ----- Source: /opt/amber11/dat/leap/cmd/leaprc.ff99SB
> ----- Source of /opt/amber11/dat/leap/cmd/leaprc.ff99SB done
> Opening /opt/amber11/dat/leap/prep/leap.log: Permission denied
> Opening /opt/amber11/dat/leap/lib/leap.log: Permission denied
> Opening /opt/amber11/dat/leap/parm/leap.log: Permission denied
> Opening /opt/amber11/dat/leap/cmd/leap.log: Permission denied
> Could not open file leap.log: system error
> Loading parameters: /opt/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: /opt/amber11/dat/leap/parm/frcmod.ff99SB
> Reading force field modification type file (frcmod)
> Reading title:
> Modification/update of parm99.dat (Hornak & Simmerling)
> Loading library: /opt/amber11/dat/leap/lib/all_nucleic94.lib
> Segmentation fault
>
>
> Besides, when I try to source gaff.dat, I get errors of the type:
>
>
> ERROR: syntax error
>
> Couldn't scan NUMBER from
> (----------------------------------------------------------------------------)
> ERROR: syntax error
>
> ERROR: syntax error
>
>
> I have tried to install the version 1.4 and also 1.3. I could not install
> properly the patch for the version 1.4, so I tried with the version 1.3, but
> this error was common in both versions.
> Do you have any idea of what is happening? Any help will be very useful.
> Thanks a lot in advance.
>
> Rebeca Garcia
> Santiago de Compostela University
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Sep 02 2010 - 06:00:05 PDT
