AMBER Archive (2005)

Subject: Re: AMBER: lib-4324 : UNRECOVERABLE library error

From: lv haiting (lhaiting_at_126.com)
Date: Wed Dec 21 2005 - 22:21:50 CST

Thomas Cheatham,
    Yes, you are right. Thank you very much!
        

======= 2005-12-22 11:18:42 ÄúÔÚÀ´ÐÅÖÐдµÀ£º=======

>
>
>> Now I did a hydrogen minimize using amber7, the input file is the following:
>>
>> Control section
>> &cntrl
>> ntpr = 5,
>> cut = 10.0,
>> ntb = 0,
>> maxcyc = 5000,
>> ncyc = 100,
>> ntr = 1,
>> imin = 1,
>> restraint_wt=500,
>> restraintmask='!@H=',
>> &end
>>
>> But the system always terminated the job abnormally, the error information is :
>>
>> lib-4324 : UNRECOVERABLE library error
>>
>> Encountered during a namelist READ from unit 5
>> Fortran unit 5 is connected to a sequential formatted text file: "minH.in"
>> IOT Trap
>> MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize()
>> MPI: aborting job
>> MPI: Received signal 6
>
>If I remember correctly, the "restaintmask" commands replacing the archaic
>GROUP input were not added until AMBER 8.0. What complicates diagnosing
>your particular problem is that the error message is not very instructive.
>
>Without knowing the history (i.e. GROUP input vs. restraintmask), I would
>first try to diagnose the problem by running the code interactively on a
>single processor (not using MPI) as a test.
>
>Anytime you see the problem "UNRECOVERABLE library error ... Encountered
>during a namelist READ" this normally means that some variable is in the
>namelist (i.e. one of the keywords specified with the &cntrl or &wt or
>other namelists) that is not recognized. It could be spelled wrong or not
>present in that version of AMBER. This problem can be particularly acute
>if you are using inputs from amber6->8 with sander versions that do not
>match as many variables changed or were deprecated. Some
>compilers/machines are graceful with respect to namelist errors; most are
>not so in normal usage you will have to systematically check.
>
>I believe however in this case that it is the restraintmask and related
>variables; for AMBER 7.0, see the GROUP input specification in the
>appendix and follow this for setting atoms to be restrained when NTR=1.
>
>
>
>
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= = = = = = = = = = = = = = = = = = = =
                        

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¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡lv haiting
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡lhaiting_at_126.com
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2005-12-22

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