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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Received on Mon Jul 30 2012 - 05:00:02 PDT
