Hi,
The relevant error message is this:
On Wed, Jul 30, 2014 at 7:46 AM, Nicole Ippolito <
ippolito.nicole89.gmail.com> wrote:
> Error: No eigenvectors data set specified ('evecs <name>'). To load
> Error: eigenvectors from a file use 'readdata <file>' prior to
> this command.
> 1 errors encountered reading input.
>
In the input I provided I referred to the file and not the data set. The
'projection' command requires that you either load or generate the evecs
data set prior to using it. The internal name you gave your modes in
'diagmatrix' is 'mymode', so you need to specify that , e.g.
crdaction crd1 projection evecs mymode out projection1-3.out start 1 stop 3
.CA myproj
Hope this helps,
-Dan
PS - The way you were doing things, the 'readdata' command should come
before 'crdaction projection' so that the modes data set is available for
the projection command.
> 100% Complete.
> TIME: Total action execution time: 102.7419 seconds.
> [runanalysis diagmatrix mymatrix out evecs.dat vecs 20 name mymode]
> Changed DataFile 'evecs.dat' type to Evecs file for set mymode
> DIAGMATRIX: Diagonalizing matrix mymatrix and writing modes to
> evecs.dat
> Calculating 20 eigenvectors
> Storing modes with name: mymode
> TIME: Total analysis execution time: 0.2025 seconds.
> [readdata evecs.dat]
> Reading 'evecs.dat' as Evecs file with name 'evecs.dat'
> Reading modes from evecs.dat
> File contains 20 modes.
> Warning: # modes to read (50) > modes in file. Only reading 20 modes.
> [crdaction crd1 projection mymodes evecs.dat out projection1-3.out start
> 1 stop 3 .CA myproj]
> TIME: Total execution time: 2174.0333 seconds.
>
>
>
> Thank you for your help,
>
> Nicole
>
>
> On Tue, Jul 29, 2014 at 10:07 AM, Nicole Ippolito <
> ippolito.nicole89.gmail.com> wrote:
>
> > Thank you for the detailed explanation and the reference. I believe it is
> > working.
> >
> > Nicole
> >
> >
> > On Tue, Jul 29, 2014 at 9:31 AM, Daniel Roe <daniel.r.roe.gmail.com>
> > wrote:
> >
> >> PS - For a concrete example of performing PCA with cpptraj see
> >> http://pubs.acs.org/doi/abs/10.1021/jp4125099 and supporting material
> >> therein.
> >>
> >> -Dan
> >>
> >>
> >> On Tue, Jul 29, 2014 at 8:16 AM, Daniel Roe <daniel.r.roe.gmail.com>
> >> wrote:
> >>
> >> > Hi,
> >> >
> >> > You're missing some elements from your script, and have a few things
> out
> >> > of order. By default in cpptraj when you specify an action or an
> >> analysis
> >> > it goes into either the action list or analysis list respectively; it
> is
> >> > not immediately executed. I will go through your input and try to
> >> explain
> >> > what's happening:
> >> >
> >> > On Fri, Jul 25, 2014 at 11:56 AM, Nicole Ippolito <
> >> > ippolito.nicole89.gmail.com> wrote:
> >> >
> >> >> trajin ~/BRAF/MD/V600E505H/sor/V600E505H_sor_aMD_0_300ns.crd.gz
> >> >> createcrd crd1
> >> >> run
> >> >>
> >> >
> >> > Here you are essentially loading a trajectory into the coords data set
> >> > named 'crd1'. The 'run' statement means "process all currently loaded
> >> > trajectories with any initialized actions", and 'createcrd' is the
> only
> >> > action set up here.
> >> >
> >> >
> >> >> rms first .CA
> >> >> reference V600E505H_sor_aMD_avg_pdb.pdb
> >> >>
> >> >
> >> > These statements seem out of order. They are placed after the run
> >> > statement, and so they are not processed until the first 'run' is
> >> > completed. Presumably your intent was to remove overall rotation and
> >> > translation from your coordinates with the 'rms' statement. If that is
> >> the
> >> > case then it should come before the createcrd statement. Also, since
> you
> >> > also have a later 'rms' command that fits to a reference, this makes
> me
> >> > think this first 'rms' was for creating an average structure to use
> as a
> >> > reference, and the 'average' command is missing.
> >> >
> >> > The 'reference' command is actually what kills the run: if you check
> >> your
> >> > output you will see the message "Error: reference: Could not set up
> >> > trajectory". This indicates that "V600E505H_sor_aMD_avg_pdb.pdb" does
> >> not
> >> > exist; perhaps you meant to create an average?
> >> >
> >> >
> >> >> crdaction crd1 rms reference .CA
> >> >> crdaction crd1 matrix out matrix.dat name mymatrix covar .CA
> >> >>
> >> > runanalysis diagmatrix mymatrix out evecs.dat vecs 20 name mymodes
> >> >>
> >> >
> >> > These statements seem fine as long as a reference is successfully
> loaded
> >> > and your 'crd1' coordinates is properly loaded.
> >> >
> >> >
> >> >> crdaction crd1 projection modes evecs.dat start 1 stop 3 .CA myproj
> >> >>
> >> >
> >> > This will not work, since you named your modes internally as 'mymodes'
> >> but
> >> > you're trying to use the file name 'evecs.dat'. Change 'evecs.dat' to
> >> > 'mymodes'.
> >> >
> >> >
> >> >> hist myproj:1 bins 200 out PC.hist.agr
> >> >> hist myproj:2 bins 200 out PC.hist.agr
> >> >>
> >> >
> >> > This seems like it should work as well.
> >> >
> >> > So to summarize, your final script should look something like this:
> >> >
> >> > trajin ~/BRAF/MD/V600E505H/sor/V600E505H_sor_aMD_0_300ns.crd.gz
> >> > # Fit to first frame for averaging
> >> > rms first .CA
> >> > # Average the trajectory
> >> > average V600E505H_sor_aMD_avg_pdb.pdb pdb
> >> > # Save the rms-fit coords
> >> > createcrd crd1
> >> > # First run
> >> > run
> >> > # Load the generated average as reference
> >> > reference V600E505H_sor_aMD_avg_pdb.pdb
> >> > # Fit saved coords to the reference
> >> > crdaction crd1 rms reference .CA
> >> > # Calculate covariance matrix from fit coords
> >> > crdaction crd1 matrix out matrix.dat name mymatrix covar .CA
> >> > # Diagonalize matrix to get eigenvectors/eigenvalues
> >> > runanalysis diagmatrix mymatrix out evecs.dat vecs 20 name mymodes
> >> > # Project fit coords along eigenvectors 1-3
> >> > crdaction crd1 projection modes evecs.dat start 1 stop 3 .CA myproj
> >> > # Set up histograms for PC projections
> >> > hist myproj:1 bins 200 out PC.hist.agr
> >> > hist myproj:2 bins 200 out PC.hist.agr
> >> > hist myproj:3 bins 200 out PC.hist.agr
> >> > # Run analyses
> >> > runanalysis
> >> >
> >> > Note that the final 'runanalysis' is not strictly necessary as cpptraj
> >> > will try to run any actions or analyses that are set up before
> quitting
> >> > when reading a script, but I include it for completeness.
> >> >
> >> > Hope this helps,
> >> >
> >> > -Dan
> >> >
> >> >
> >> >
> >> >
> >> >>
> >> >>
> >> >> CPPTRAJ: Trajectory Analysis. V14.01
> >> >> ___ ___ ___ ___
> >> >> | \/ | \/ | \/ |
> >> >> _|_/\_|_/\_|_/\_|_
> >> >> Reading 'parm' as Amber Topology
> >> >> INPUT: Reading Input from STDIN
> >> >> [trajin ~/BRAF/MD/V600E505H/sor/V600E505H_sor_aMD_0_300ns.crd.gz ]
> >> >> Reading
> >> >> '/home/aubndi/BRAF/MD/V600E505H/sor/V600E505H_sor_aMD_0_300ns.crd.gz'
> >> as
> >> >> Amber Trajectory
> >> >> [createcrd crd1 ]
> >> >> CREATECRD: Saving coordinates from Top parm to "crd1"
> >> >> [run]
> >> >> ---------- RUN BEGIN
> -------------------------------------------------
> >> >>
> >> >> PARAMETER FILES:
> >> >> 0: 'parm', 36610 atoms, 11002 res, box: Orthogonal, 10731 mol, 10722
> >> >> solvent, 60000 frames
> >> >>
> >> >> INPUT TRAJECTORIES:
> >> >> 0: 'V600E505H_sor_aMD_0_300ns.crd.gz' is an AMBER trajectory, Parm
> >> parm
> >> >> (Orthogonal box) (reading 60000 of 60000)
> >> >> Coordinate processing will occur on 60000 frames.
> >> >> TIME: Run Initialization took 0.0000 seconds.
> >> >>
> >> >> BEGIN TRAJECTORY PROCESSING:
> >> >> .....................................................
> >> >> ACTION SETUP FOR PARM 'parm' (1 actions):
> >> >> 0: [createcrd crd1 ]
> >> >> ----- V600E505H_sor_aMD_0_300ns.crd.gz (1-60000, 1) -----
> >> >> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% Error: reference: Could not
> >> set up
> >> >> trajectory.
> >> >> 1 errors encountered reading input.
> >> >> 100% Complete.
> >> >>
> >> >> Read 60000 frames and processed 60000 frames.
> >> >> TIME: Trajectory processing: 1743.3814 s
> >> >> TIME: Avg. throughput= 34.4159 frames / second.
> >> >>
> >> >> ACTION OUTPUT:
> >> >>
> >> >> DATASETS:
> >> >> 1 data set:
> >> >> crd1 "crd1" (coordinates), size is 60000 (25138 MB) Box
> Coords,
> >> >> 36610 atoms
> >> >> ---------- RUN END
> ---------------------------------------------------
> >> >> [rms first .CA]
> >> >> RMSD: (.CA), reference is first frame (.CA), with fitting.
> >> >> [reference V600E505H_sor_aMD_avg_pdb.pdb]
> >> >> TIME: Total execution time: 1743.8619 seconds.
> >> >> _______________________________________________
> >> >> AMBER mailing list
> >> >> AMBER.ambermd.org
> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> >
> >> >
> >> >
> >> > --
> >> > -------------------------
> >> > 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) 585-6208 (Fax)
> >> >
> >>
> >>
> >>
> >> --
> >> -------------------------
> >> 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) 585-6208 (Fax)
> >> _______________________________________________
> >> 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
>
--
-------------------------
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) 585-6208 (Fax)
_______________________________________________
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 30 2014 - 07:30:02 PDT
