Re: [AMBER] tleap and xleap problem in loading mol2 files

From: Jason Swails <>
Date: Fri, 12 Mar 2010 00:10:02 -0500


On Thu, Mar 11, 2010 at 11:51 PM, <> 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 M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Thu Mar 11 2010 - 21:30:04 PST
Custom Search