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 - 00:00:02 PDT
