Alex,
Tleap should work fine for the things you said you're trying. But,
you do need to use sleap because otherwise you won't get the 1-4
scaling right. The scaling is no longer specified in the mdin file.
I just tried with my install of amber11/tleap, and it works. Sleap
works, too. There is most likely something wrong with your install or
compiler or something. What machine? What linux? What compilers?
New machine? Could there be disk issues? A seg fault doesn't tell
much by itself.
On Fri, May 21, 2010 at 1:14 PM, Jason Swails <jason.swails.gmail.com> wrote:
> 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
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Fri May 21 2010 - 10:30:08 PDT
