AMBER Archive (2009)

Subject: [AMBER] RE: MM-PBSA test jobs error messages (with bugfix.all)

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Wed Jul 29 2009 - 00:50:50 CDT

Dear Ray,

 

Yes, I have already done this according to the manual of AMBER10, as follows:

 

Go to the Amber web site, http://amber.scripps.edu, and download any bug fixes for version
10 that may have been posted. There will be a file called "bugfix.all", which is used
as follows:
cd $AMBERHOME
patch -p0 -N -r patch-rejects < bugfix.all

 

It was done two months ago. What should I do to correct this error?

 

Best regards,

Cat

 
> Date: Wed, 29 Jul 2009 11:33:21 +0800
> Subject: Re: MM-PBSA test jobs error messages
> From: ray.luo_at_uci.edu
> To: askamber23_at_hotmail.com
>
> Did you patch all the bugfixes? If not, please patch those fixes,
> especially the mmpbsa one and try again.
>
> All the best,
> Ray
>
> 2009/7/28 Catein Catherine <askamber23_at_hotmail.com>:
> > 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_at_uci.edu
> >> To: askamber23_at_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_at_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_at_uci.edu
> >> > To: askamber23_at_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_at_uci.edu <mailto:rluo_at_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
> >> >
> >> >
> >> >
> >> > ------------------------------------------------------------------------
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