Dear Ray,
I did the analysis one by one (mm_pbsa.pl xxx.in > xxx.out) in the mm_pbsa directory.
For 01_GenerateSnapshots directory: No problem.
For 02_MMPBSA_Stability directory: No skew or curtosis when zero variance in moment appear. results in ras_raf_II_wt_statistics.out equals to ras_raf_II_wt_statistics.out.save
For 03_MMPBSA_Binding directory: message below appears:
Use of uninitialized value in multipliation (*) at /home/amber10/src/mm_pbsa/mm_pbsa_statics.pm line 1418
........similar sentences, with different number at the end..............................
No data for 0+1 MM ELE 3
At the end of the mm_pbsa.log file, the file stopped at =>> Calc delta from raw data. I cannot find the ras_raf_II_wt_statistics.out file.
What should I do to correct this error?
Best regards,
Cat
> Date: Mon, 27 Jul 2009 17:59:45 +0800
> From: ray.luo.uci.edu
> To: askamber23.hotmail.com
> Subject: Re: MM-PBSA cannot finish. Out files attached.
>
> Dear Cat,
>
> I see several problems ...
>
> 1) Why there are 100 snapshots in the log file, but there are only ten
> in the energy output files.
> 2) There is a redundant entry for snapshot #1, indicating you ran it
> twice without completely cleaning up the folder.
> 3) The nmode run failed, looks that your memory is not enough. Can you
> try something smaller to see whether you can run it? 4) How about all
> the examples in $AMBERHOME/src/mmpbsa? Can you run it without any problem?
>
> All the bset,
> Ray
>
> ==========================================
> Ray Luo, Ph.D.
> Associate Professor
> Dept Molecular Biology & Biochemistry
> University of California, Irvine, CA 92697
> USPS: PO Box 3900 Email: rluo.uci.edu
> Phones: (949) 824-9528, 9562
> Web: http://rayl0.bio.uci.edu/
> ==========================================
>
>
>
> Catein Catherine wrote:
> > Dear Ray,
> >
> > The output files are attached. please kindly instruct what's wrong
> > with the results?
> >
> > I did the "pbsa_decpw/decres/dmp/pgb/radi/trx/tsr" in the test
> > directory. But no error message (diff) appeared.
> >
> > Best regards,
> >
> > Cat.
> >
> >
> >
> >
> >
> > ------------------------------------------------------------------------
> >
> >
> >
> >
> > Date: Sat, 25 Jul 2009 07:50:02 +0800
> > From: ray.luo.uci.edu
> > To: askamber23.hotmail.com
> > Subject: Re: MM-PBSA cannot finish without error message.
> >
> > Can you run all the examples within the mmpbsa directory?
> >
> > Also, it would be really helpful you if you can attach the "*.out"
> > files. These files contains more detailed info of your runs.
> >
> > Ray
> >
> > ==========================================
> > Ray Luo, Ph.D.
> > Associate Professor
> > Dept Molecular Biology & Biochemistry
> > University of California, Irvine, CA 92697
> > USPS: PO Box 3900 Email: rluo.uci.edu <mailto:rluo.uci.edu>
> > Phones: (949) 824-9528, 9562
> > Web: http://rayl0.bio.uci.edu/
> > ==========================================
> >
> >
> >
> > Catein Catherine wrote:
> >
> > Dear All,
> >
> > I am using AMBER10 as well. I also face some problem when do the
> > mm_gbsa calculation with the following input files.
> >
> > All the patch has been installed, no error message was found after
> > I the installation test.
> >
> > could you mind to let me know what should I do next to correct
> > this error?
> >
> > Best regards,
> >
> > Cat
> >
> >
> >
> > ------------------------------------------------------------------------
> > Share your memories online with anyone you want anyone you want.
> > <http://www.microsoft.com/middleeast/windows/windowslive/products/photos-share.aspx?tab=1>
> >
> >
> > ------------------------------------------------------------------------
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> > <http://www.microsoft.com/windows/windowslive/default.aspx>
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Received on Tue Jul 28 2009 - 10:07:38 PDT
