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-- 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 >> >> >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Mon Jul 30 2012 - 04:00:02 PDT