Hi,
2011/7/5 Giorgos Lamprinidis <lamprinidis.pharm.uoa.gr>:
> Dan, thanks for your reply, however ambertools 1.5 is compatible with
> amber10? And if I do so, I must have amber10 folder for running sander,
> pmemd etc, and amber11 folder for running ambertools? or I must combine them
> just after I compile them?
Definitely DO NOT combine the amber11 and amber10 folders, they are
not compatible. That being said, your system can exist quite happily
with an amber10 folder for compiling/running sander/pmemd, and an
amber11 folder for doing everything else. Just make sure your
AMBERHOME environment variable is pointing to the amber11 directory
since it's really only the AmberTools programs that need it.
If you run into any more problems let me know.
-Dan
>
> Dr George Lamprinidis
>
> -----Original Message-----
> From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
> Sent: Tuesday, July 05, 2011 6:44 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] segmentation fault on tleap
>
> Hi,
>
> The best solution may be to upgrade to the latest version of
> AmberTools, 1.5 (http://ambermd.org/AmberTools-get.html). It contains
> many improvements and fixes to almost every part of the AmberTools
> codebase.
>
> -Dan
>
> On Tue, Jul 5, 2011 at 11:32 AM, Giorgos Lamprinidis
> <lamprinidis.pharm.uoa.gr> wrote:
>> Dear Amber users,
>>
>> Some months ago i installed successfully ambertools 1.2 on a quad core
>> computer running fedora 11.
>> Now i have a new computer running Fedora core 15 (64bit). I tried to
>> compile ambertools. I had some problems but finally i compiled AT 1.2
>> without significant errors. However when i try to "source" leaprd.ff99SB
>> tleap crashes giving the next error:
>>
>> [gl.localhost gl]# $AMBERHOME/exe/tleap -f leaprc.ff99SB
>> -I: Adding /opt/amber10/dat/leap/prep to search path.
>> -I: Adding /opt/amber10/dat/leap/lib to search path.
>> -I: Adding /opt/amber10/dat/leap/parm to search path.
>> -I: Adding /opt/amber10/dat/leap/cmd to search path.
>> -f: Source leaprc.ff99SB.
>> Welcome to LEaP!
>> (no leaprc in search path)
>> Sourcing: /opt/amber10/dat/leap/cmd/leaprc.ff99SB
>> Log file: ./leap.log
>> Loading parameters: /opt/amber10/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/amber10/dat/leap/parm/frcmod.ff99SB
>> Reading force field modification type file (frcmod)
>> Reading title:
>> Modification/update of parm99.dat (Hornak & Simmerling)
>> Loading library: /opt/amber10/dat/leap/lib/all_nucleic94.lib
>> /opt/amber10//exe/tleap: line 8: 29298 Segmentation fault (core
>> dumped) /opt/10/bin/teLeap -I/opt/amber10/dat/leap/prep
>> -I/opt/amber10/dat/leap/lib -I/opt/amber10/dat/leap/parm
>> -I/opt/amber10/dat/leap/cmd $*
>>
>> Next i tried to copy the whole "amber10" directory from the old pc to the
>> new one. I still get the same segmentation fault.
>> Does anyone has the same problem? How can i figure out what goes wrong?
>> It may be some libraries i must install to bypass this error?
>> Any help would me gvaluable.
>>
>> Yours
>> Dr George Lamprinidis
>>
>>
>>
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Tue Jul 05 2011 - 09:30:07 PDT
