On Fri, May 21, 2010 at 1:09 PM, Alex Boncheff <abonchef.uoguelph.ca> wrote:
> Hi all,
>
> I've been having problems loading parameters into leap. I hope this
> explains the issue:
>
> user.computer:~/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.GLYCAM_06
> ----- Source: /opt/amber11/dat/leap/cmd/leaprc.GLYCAM_06
> ----- Source of /opt/amber11/dat/leap/cmd/leaprc.GLYCAM_06 done
> Loading parameters: /opt/amber11/dat/leap/parm/GLYCAM_06f.dat
> Reading title:
> GLYCAM PARAMETERS (FOR AMBER 8.0, RESP 0.010), COPYRIGHT CCRC 2004
> Loading Prep file: /opt/amber11/dat/leap/prep/GLYCAM_06.prep
> Loading library: /opt/amber11/dat/leap/lib/GLYCAM_amino_06.lib
> Segmentation fault
> user.computer:~/opt/amber11/exe$
>
> Additionally...
>
> I'm getting errors when I try to set the head and tail atoms of a residue.
> It tells me it's not an "atom type" when I try to set a particular atom that
> I know for sure should work. Overall I've reinstalled the program and then
> even reinstalled linux when that didn't work.
>
> Ideas?
>
There have been issues reported with tleap (involving segfaults), and
they're a little tricky to track down. Try sleap. Does that help? (sleap
is intended to replace tleap, anyway, so moving over to that I think is
ultimately better)
All the best,
Jason
> Thanks
>
> --
> Alex Boncheff
> MSc. Candidate
> Department of Chemistry
> University of Guelph
> Guelph, ON, Canada
> N1G 2W1
>
> Office: MacNaughton 233
> T: 519-824-4120 x 58111
>
>
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> 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 Fri May 21 2010 - 10:30:05 PDT
