I think that pbsa (or sander?) program fails to produce results.
Attached are the output files from amber11/test/sander_pbsa_dmp, you can
see that output is just truncated. mm_pbsa.pl leads to a similar fail:
.out file ends with
======== Implicit Solvent Initialization ========
Max Nonbonded Pairs: 2935926 72987362
and console says:
> mm_pbsa.pl binding_energy.mmpbsa > nrg.log
Use of uninitialized value $inp in concatenation (.) or string at
/opt/amber11/src/mm_pbsa/mm_pbsa_createinput.pm line 596.
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
sander 083E397B 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 B6D41C0E Unknown Unknown Unknown
/opt/amber11/bin/sander -O -i pbsa_rec.in -o pbsa_rec.1.out -c
./snapshots/snapshot_rec.crd.1 -p ./103_84.prmtop not successful
For details see:
http://ambermd.org/Questions/mm_pbsa.html#pbsa_command_not_successful
All other tests are passed, only two of them lead to numerical differences.
On 04/19/2011 07:18 PM, Jason Swails wrote:
> 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
>>
>
>
>
--
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
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Received on Tue Apr 19 2011 - 09:00:02 PDT
