Dear Ray,
I found I got 21 bug fixed in my early version of Bugfix.all file.
Is it a must to recompile the amber all over again to fix the problem? I got most of the PBSA related bug fixed, except bugfix.23.
Best regards,
Cat
> Date: Wed, 29 Jul 2009 14:31:43 +0800
> Subject: Re: MM-PBSA test jobs error messages (with bugfix.all)
> From: ray.luo.uci.edu
> To: askamber23.hotmail.com
>
> Cat,
>
> I'm not sure you patched the latest bugfix files ...
>
> The mmpbsa bugfix was released just several months ago, so it's likely
> that you haven't patch the bugfix for it. You can read your bugfix.all
> file to see which fixes are included in your last patch. So please go
> to the web site again to see which bugfix files you have not patched
> and download and patch them.
>
> I'm sorry this is generating confusion among end users since we can
> only release bugfixes when people report them, and they are not caught
> at the same time.
>
> All the best,
> Ray
>
> On Wed, Jul 29, 2009 at 1:50 PM, Catein Catherine<askamber23.hotmail.com> wrote:
> > 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.uci.edu
> >> To: askamber23.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.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.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
> >> >> >
> >> >> >
> >> >> >
> >> >> >
> >> >> > ------------------------------------------------------------------------
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Received on Wed Aug 19 2009 - 19:38:31 PDT
