Hello,
On Thu, Mar 11, 2010 at 11:51 PM, <d96543015.ntu.edu.tw> wrote:
> Dear Amber users
>
> I was trying to load mol2 files into tleap and xleap. However, tleap and
> xleap crashed immediately after I typed "loadmol2 db2clean01.mol2" with the
> following error output:
>
>> loadmol2 db2clean01.mol2
>
> Loading Mol2 file: ./db2clean01.mol2
> Reading MOLECULE named UNK
> /home/shih-di/bin/amber10/exe/tleap: line 8: 7595 Segmentation fault
> /home/shih-di/bin/amber10/bin/teLeap
> -I/home/shih-di/bin/amber10/dat/leap/prep
> -I/home/shih-di/bin/amber10/dat/leap/lib
> -I/home/shih-di/bin/amber10/dat/leap/parm
> -I/home/shih-di/bin/amber10/dat/leap/cmd $*
>
> The mol2 and original pdb file is enclosed. The mol2 file was prepared using
> antechamber because I planed to use GAFF force field. Could anyone tell me
> why tleap and xleap vrashed? I got no problem loading sustiva.mol2 in the
> example.
I couldn't reproduce your error... The loadmol2 command worked just
fine for me in tleap/xleap. However, you have to assign a loaded mol2
to a variable, i.e.
LIG = loadmol2 db2clean01.mol2
in order for it to appear on the list of available units. (but even
without the assignment above I didn't get a segfault).
It may be worth trying to rebuild leap and see if it works then.
Good luck!
Jason
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Mar 11 2010 - 21:30:04 PST
