AMBER Archive (2005)

Subject: AMBER: MM_PBSA problem

From: Xin Hu (hux_at_mail.rockefeller.edu)
Date: Tue Apr 12 2005 - 11:09:36 CDT

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_at_bioinformatik.uni-frankfurt.de>
To: <amber_at_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_at_bioinformatik.uni-frankfurt.de>
>> To: <amber_at_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
>> > -----------------------------------------------------------------------
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