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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 02 2010 - 05:30:03 PDT
