Then these are to be expected, I think. PBSA changed a little bit from 1.4
to 1.5, and one of those changes was removing (changing) namelist input
variables. If you look closely at the output files created by those tests,
I think you'll see that's the case. You will also see numerical differences
crop up in several other tests, causing them to "fail". Rest assured,
everything is fine and PBSA is behaving as expected. Just make sure it
passes the PBSA tests in $AMBRHOME/AmberTools/test.
HTH,
Jason
On Tue, Apr 19, 2011 at 8:12 AM, Dmitry Osolodkin <divanych.rambler.ru>wrote:
> 1.5
>
> On 04/19/2011 07:12 PM, Jason Swails wrote:
> > Did you install Amber11 alongside AmberTools 1.5 or 1.4?
> >
> > On Tue, Apr 19, 2011 at 5:42 AM, Dmitry Osolodkin<divanych.rambler.ru
> >wrote:
> >
> >> Dear AMBER List,
> >>
> >> I've just upgraded to AMBER 11 and trying to perform MM-PBSA
> >> calculations. Unfortunately, it seems that pbsa is compiled incorrectly:
> >> tests say something like following:
> >>
> >> ==============================================================
> >> cd sander_pbsa_dmp&& ./Run.dmp.min
> >> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> >> Image PC Routine Line Source
> >>
> >> sander 083E3947 Unknown Unknown Unknown
> >> sander 080FA517 Unknown Unknown Unknown
> >> sander 080CBCCA Unknown Unknown Unknown
> >> sander 080CABAB Unknown Unknown Unknown
> >> sander 0804F244 Unknown Unknown Unknown
> >> libc.so.6 40989C0E Unknown Unknown Unknown
> >> ./Run.dmp.min: Program error
> >> make[1]: [test.pbsa] Error 1 (ignored)
> >> cd sander_pbsa_ipb2&& ./Run.110D.min
> >> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> >> Image PC Routine Line Source
> >>
> >> sander 083E3947 Unknown Unknown Unknown
> >> sander 080FA517 Unknown Unknown Unknown
> >> sander 080CBCCA Unknown Unknown Unknown
> >> sander 080CABAB Unknown Unknown Unknown
> >> sander 0804F244 Unknown Unknown Unknown
> >> libc.so.6 40989C0E Unknown Unknown Unknown
> >> ./Run.110D.min: Program error
> >> make[1]: [test.pbsa] Error 1 (ignored)
> >> cd sander_pbsa_delphi&& ./Run.1az6.min
> >> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> >> Image PC Routine Line Source
> >>
> >> sander 083E3947 Unknown Unknown Unknown
> >> sander 080FA517 Unknown Unknown Unknown
> >> sander 080CBCCA Unknown Unknown Unknown
> >> sander 080CABAB Unknown Unknown Unknown
> >> sander 0804F244 Unknown Unknown Unknown
> >> libc.so.6 40989C0E Unknown Unknown Unknown
> >> ./Run.1az6.min: Program error
> >> make[1]: [test.pbsa] Error 1 (ignored)
> >> cd sander_pbsa_lpb&& ./Run.lsolver.min
> >> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> >> Image PC Routine Line Source
> >>
> >> sander 083E3947 Unknown Unknown Unknown
> >> sander 080FA517 Unknown Unknown Unknown
> >> sander 080CBCCA Unknown Unknown Unknown
> >> sander 080CABAB Unknown Unknown Unknown
> >> sander 0804F244 Unknown Unknown Unknown
> >> libc.so.6 40989C0E Unknown Unknown Unknown
> >> ./Run.lsolver.min: Program error
> >> make[1]: [test.pbsa] Error 1 (ignored)
> >> cd sander_pbsa_radi&& ./Run.ion.min
> >> diffing ./out.save/Li.out.save with Li.out
> >> PASSED
> >> ==============================================================
> >>
> >> I use Intel compilers (composerxe-2011.2.137) on 32-bit machine. What
> >> can I do to beat this error?
> >>
> >> Best regards,
> >> Dmitry
> >> --
> >> Dmitry Osolodkin
> >> Researcher
> >> Group of Computational Molecular Design
> >> Department of Chemistry
> >> Moscow State University
> >> Moscow 119991 Russia
> >> e-mail: dmitry_o.qsar.chem.msu.ru
> >> Phone: +7-495-9393557
> >> Fax: +7-495-9390290
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
>
> --
> Dmitry Osolodkin
> Researcher
> Group of Computational Molecular Design
> Department of Chemistry
> Moscow State University
> Moscow 119991 Russia
> e-mail: dmitry_o.qsar.chem.msu.ru
> Phone: +7-495-9393557
> Fax: +7-495-9390290
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Apr 19 2011 - 08:30:08 PDT
