Thanks you Jason.
> From: jason.swails.gmail.com
> Date: Mon, 30 Jul 2012 09:14:31 -0400
> To: amber.ambermd.org
> Subject: Re: [AMBER] How to install bugfix.16 specifically?
>
> They both install together. Follow the installation instructions in the AmberTools manual.
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
> On Jul 30, 2012, at 7:31 AM, Catein Catherine <askamber23.hotmail.com> wrote:
>
> >
> > Dear Jason,
> > Should re reinstall AMBERTools only or should I also resinstall AMBER12?
> > Best regards,
> > Cat
> >
> >> From: jason.swails.gmail.com
> >> Date: Mon, 30 Jul 2012 06:32:32 -0400
> >> To: amber.ambermd.org
> >> Subject: Re: [AMBER] How to install bugfix.16 specifically?
> >>
> >> You need to configure in serial and compile again.
> >>
> >> --
> >> Jason M. Swails
> >> Quantum Theory Project,
> >> University of Florida
> >> Ph.D. Candidate
> >> 352-392-4032
> >>
> >> On Jul 30, 2012, at 2:37 AM, Catein Catherine <askamber23.hotmail.com> wrote:
> >>
> >>>
> >>> Dear AMBER users,
> >>>
> >>> I have tried to use the following command to apply bugfix16 specifically. However, it seem reconfirmed that bugfix16 has been installed.
> >>>
> >>> Did I do anything wrong, as I still found when I do cpptraj for the following cpptraj file, error message of autoimage command is not found.
> >>>
> >>> trajin ./md35.mdcrd
> >>> autoimage
> >>> trajout md35_cpptraj.netcdf netcdf
> >>> rms first out md35_cpptraj_all.rms .CA,C1'
> >>> average md35_cpptraj_average_nobox.pdb pdb nobox
> >>>
> >>> What's wrong with my cpptraj file? Could you please kindly help to point out my error. Many thanks.
> >>>
> >>> Best regards,
> >>>
> >>> Catherine
> >>>
> >>>
> >>> ====================================================================
> >>>
> >>> [root.cmc01 amber12]# ./patch_amber.py --apply bugfix/bugfix.16
> >>> Applying patch bugfix/bugfix.16:
> >>> Error or warning during patching process for bugfix/bugfix.16:
> >>> Reversed (or previously applied) patch detected! Skipping patch.
> >>> 3 out of 3 hunks ignored -- saving rejects to file AmberTools/src/cpptraj/src/ActionList.cpp.rej
> >>> The next patch would create the file AmberTools/src/cpptraj/src/Action_AutoImage.cpp,
> >>> which already exists! Skipping patch.
> >>> 1 out of 1 hunk ignored -- saving rejects to file AmberTools/src/cpptraj/src/Action_AutoImage.cpp.rej
> >>> The next patch would create the file AmberTools/src/cpptraj/src/Action_AutoImage.h,
> >>> which already exists! Skipping patch.
> >>> 1 out of 1 hunk ignored -- saving rejects to file AmberTools/src/cpptraj/src/Action_AutoImage.h.rej
> >>> Reversed (or previously applied) patch detected! Skipping patch.
> >>> 1 out of 1 hunk ignored -- saving rejects to file AmberTools/src/cpptraj/src/Action_Center.cpp.rej
> >>> Reversed (or previously applied) patch detected! Skipping patch.
> >>> 3 out of 3 hunks ignored -- saving rejects to file AmberTools/src/cpptraj/src/Action_Image.cpp.rej
> >>> Reversed (or previously applied) patch detected! Skipping patch.
> >>> 1 out of 1 hunk ignored -- saving rejects to file AmberTools/src/cpptraj/src/Action_Image.h.rej
> >>> Reversed (or previously applied) patch detected! Skipping patch.
> >>> 2 out of 2 hunks ignored -- saving rejects to file AmberTools/src/cpptraj/src/Frame.cpp.rej
> >>> Reversed (or previously applied) patch detected! Skipping patch.
> >>> 1 out of 1 hunk ignored -- saving rejects to file AmberTools/src/cpptraj/src/Frame.h.rej
> >>> Reversed (or previously applied) patch detected! Skipping patch.
> >>> 2 out of 2 hunks ignored -- saving rejects to file AmberTools/src/cpptraj/src/cpptrajdepend.rej
> >>> Reversed (or previously applied) patch detected! Skipping patch.
> >>> 3 out of 3 hunks ignored -- saving rejects to file AmberTools/src/cpptraj/src/cpptrajfiles.rej
> >>> Reversed (or previously applied) patch detected! Skipping patch.
> >>> 1 out of 1 hunk ignored -- saving rejects to file AmberTools/src/cpptraj/src/main.cpp.rej
> >>>
> >>>
> >>> Quitting in error!
> >>> [root.xxx amber12]#
> >>> ====================================================================
> >>>
> >>>> From: askamber23.hotmail.com
> >>>> To: amber.ambermd.org
> >>>> Date: Mon, 30 Jul 2012 12:29:10 +0800
> >>>> Subject: [AMBER] How to install bugfix.16 specifically?
> >>>>
> >>>>
> >>>> Dear Jason and Dan,
> >>>>
> >>>> Thank you very much for your help.
> >>>>
> >>>> I firstly install patches.
> >>>> ===================================================================
> >>>> [root.xxx amber12]# $AMBERHOME/patch_amber.py --update-tree
> >>>> Determining patches to download for AmberTools12
> >>>> AmberTools12 is up to date. Nothing to download
> >>>>
> >>>> Determining patches to download for Amber12
> >>>> Amber12 is up to date. Nothing to download
> >>>> ===================================================================
> >>>>
> >>>> Then I run cpptraj with autoimage, However, it still said, autoimage command is not known.
> >>>> ===================================================================
> >>>> CPPTRAJ: Trajectory Analysis. V12.1
> >>>> ___ ___ ___ ___
> >>>> | \/ | \/ | \/ |
> >>>> _|_/\_|_/\_|_/\_|_
> >>>>
> >>>> INPUT: Reading Input from STDIN, type "go" to run, "quit" to exit:
> >>>>> [trajin ./md35.mdcrd]
> >>>> [md35.mdcrd] contains 2500 frames.
> >>>>> [autoimage]
> >>>> Warning: Unknown Command autoimage.
> >>>>> [trajout md35_cpptraj.netcdf netcdf]
> >>>>> [rms first out md35_cpptraj_all.rms .CA,C1']
> >>>>> [average md35_cpptraj_average_nobox.pdb pdb nobox]
> >>>>>
> >>>> INPUT TRAJECTORIES:
> >>>> [md35.mdcrd] is an AMBER trajectory, Parm 0 (with box info) (reading 2500 of 2500)
> >>>> Coordinate processing will occur on 2500 frames.
> >>>> ===================================================================
> >>>>
> >>>> I guess I have updated all the patches, should I do additional step to install bugfix.16.
> >>>>
> >>>> However, I don't know how to specifically install bugfix.16. I have already download bugfix.16 to my $AMBERHOME directory. What should I do next?
> >>>>
> >>>> Best regards,
> >>>>
> >>>> Catherine
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
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> >>>
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Received on Mon Jul 30 2012 - 07:30:02 PDT
