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-- 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 >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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/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 - 06:30:02 PDT