Em Tue, 12 Apr 2005 12:09:36 -0400
"Xin Hu" <hux.mail.rockefeller.edu> escreveu:
> Hi Holger,
> Thank you for your help. I re-compiled the "serial"
>sander and run for MM_PBSA, as you suggested, it works
>well.
> But I got a problem in the next step of calculation the
>entropy using N-mode. I do not know what's the problem,
>it seems to be stuck there on the "Calc entropy" after
>minimize the first structure. I attached all the
>input/output of the minmization file and nmode files.
>Could you please look over to figure out the problem?
>
> Thank you very much for your help.
>
> Xin
>
> ---
>
>
>
> ----- Original Message ----- From: "Holger Gohlke"
><gohlke.bioinformatik.uni-frankfurt.de>
> To: <amber.scripps.edu>
> Sent: Tuesday, April 12, 2005 2:30 AM
> Subject: Re: AMBER: MM_PBSA error
>
>
>> Xin Hu schrieb:
>>>
>>> Hi Holger,
>>> Thank you very much for your help. I looked over out
>>>sander program and
>>> there is only one parallel executable of "sander" (when
>>>I compiled the
>>> parallel version, it replaced the 'serial' version of
>>>sander). (Actually
>>> this version is both working for single and multiple
>>>processors.)
>>>
>>> As you suggested, should I go ahead to re-compile a
>>>"serial" amber
>>> again
>>> and get a "single-CPU sander" (named sander_serial)? so
>>>I can specify in
>>> the
>>> mm_pbsa.in file: SANDER
>>>/usr/local/amber8/exe/sander_serial". I will try
>>> to
>>> re-compile and let you know the result.
>>
>> Yes, this is what I would do.
>>
>> Best regards
>>
>> Holger
>>
>>>
>>> Thanks,
>>>
>>> Xin
>>>
>>> ---
>>>
>>> ----- Original Message -----
>>> From: "Holger Gohlke"
>>><gohlke.bioinformatik.uni-frankfurt.de>
>>> To: <amber.scripps.edu>
>>> Sent: Monday, April 11, 2005 4:49 PM
>>> Subject: Re: AMBER: MM_PBSA error
>>>
>>> > Hi,
>>> >
>>> > I think the problem is that the sander version that is
>>>called by
>>> > mm_pbsa
>>> > is the parallel version, which requires to set
>>>"mpirun" or the like in
>>> > front of the sander call. You should be able to
>>>circumvent this by
>>> > adding a line "SANDER
>>><path_to_a_one_processor_version_of_sander>" to
>>> > the end of the mm_pbsa.in file (in the section
>>>.PROGRAMS).
>>> >
>>> > Best regards
>>> >
>>> > Holger
>>> >
>>> >
>>> >
>>> > Xin Hu schrieb:
>>> >
>>> > Dear Amber user
>>> >
>>> > I have a problem with the MM_PBSA calculation. I
>>>followed the examples
>>> > in /src/mm_pbsa/example/02_MMPBSA_Stability to run the
>>>calculation on
>>> > entropy energies,
>>> >
>>> > it showed an error:
>>> >
>>> > =>> Calculating energy / entropy contributions
>>> > Calc contrib for
>>>../01_GenerateSnapshots/ras_raf_II_wt_com.crd.1
>>> > Calc MM/GB/SAS
>>> >
>>> > Unit 6 Error on OPEN: sander_com.1.out
>>> > [0] MPI Abort by user Aborting program !
>>> > [0] Aborting program!
>>> > p0_14716: p4_error: : 1
>>> > /usr/local/amber8/exe/sander -O -i
>>>sander_com.in -o
>>> > sander_com.1.out -c
>>>../01_GenerateSnapshots/ras_raf_II_wt_com.crd.1 -p
>>> > ../ras_raf_II_wt.prmtop not successful
>>> >
>>> > I was aware that if I ingore the path specified in the
>>>command, or I
>>> > add
>>> > the full path (the working directory) to the output
>>>files, it works
>>> > properly.
>>> >
>>> > So I tried to modify the script in src/mm_pbsa, the
>>>script
>>> > "mm_pbsa_util.pm" or "mm_pbsa_calceneent.pm",
>>>attemping to delete the
>>> > path associated with command "sander", or adding
>>> >
>>> > path to the output file, however, neither way is
>>>working with errors
>>> > showing "compilation failed" "strict subs" etc.
>>> >
>>> > I wonder if anyone has caught the same problem and I
>>>appreciate for
>>> > help. The Amber8 is runnung on a linux cluster with
>>>MPI on parallel.
>>> >
>>> > Thanks,
>>> >
>>> > Xin
>>> >
>>>-----------------------------------------------------------------------
>>> > The AMBER Mail Reflector
>>> > To post, send mail to amber.scripps.edu
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>>>majordomo.scripps.edu
>>> >
>>>
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>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
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>>
Experience is what you get when you don't get what you
want.
-- Dan Stanford--
Did you compile nmode with double_precision?
maybe its the solution for your problem.
I have got the same problem some time ago.
Cheers
Nelson Fonseca
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Received on Tue Apr 12 2005 - 17:53:01 PDT
