Hi,
Could you please send me (off-list) your topology file and a
corresponding restart/PDB file containing the problem frame so I can
try and troubleshoot this? Thanks.
-Dan
On Tue, Jul 31, 2012 at 1:17 AM, Catein Catherine
<askamber23.hotmail.com> wrote:
>
> 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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>> > >>>> AMBER.ambermd.org
>> > >>>> http://lists.ambermd.org/mailman/listinfo/amber
>> > >>>
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>> > >>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Tue Jul 31 2012 - 07:00:03 PDT
