Dear All,
I have done the autoimage with cpptraj
trajin ./md35.mdcrdautoimagetrajout md35_cpptraj.netcdf netcdfrms first out md35_cpptraj_all.rms .CA,C1'average md35_cpptraj_average_nobox.pdb pdb nobox
I found the rms is jumping but the pattern is different from the results that I obtained from ptraj.
When I look at the pdb file, I found one of my protein is separated far apart.
As I am working on a protein with 4 proteins, should use autoimage my specifying only a small portion of the proteins, i.e. residue 100-200.
However, how to do it? I found "Error: Anchor mask [:100-200] corresponds to 0 mols, should only be 1." when I use the
autoimage :100-200
Any suggestions?
Unlucky Cat.......
> From: askamber23.hotmail.com
> To: amber.ambermd.org
> Date: Mon, 30 Jul 2012 22:16:47 +0800
> Subject: Re: [AMBER] How to install bugfix.16 specifically?
>
>
> 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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Received on Tue Jul 31 2012 - 00:30:02 PDT
