Yep this worked after removing the corrupted frames.
I have two trivial questions. Is it possible to look at contribution of
individual residues to the PCs (from the PCA analyses)? My second question
is whether there is a simple way to output selected frame numbers (e.g.
with an index number or select a frame which meets specific criteria) to
another trajectory?
Many thanks,
Neha
On 27 September 2016 at 22:42, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Tue, Sep 27, 2016 at 12:09 AM, Neha Gandhi <n.gandhiau.gmail.com>
> wrote:
> > I tried according to your suggestion (Run1) using serial version of
> > cpptraj. The program runs without any errors (see blow)
>
> You actually do get some warnings about corrupt frames, e.g.:
>
> > Warning: Frame 37873 coords 1 & 2 overlap at origin; may be corrupt.
>
> You should visualize these frames to make sure everything is OK. If
> they are indeed corrupt you should exclude them from this calculation
> (via 'check skipbadframes <mask>', where <mask> includes all atoms you
> care about).
>
> > but the output
> > files dihcovar.dat and modes.dihcovar.dat has NaN NaN..
>
> This could be related to your corrupted frames.
>
> -Dan
>
> >
> > I used the same trajectory in CARMA program to calculate dPCA and it
> works.
> >
> > Regards,
> > Neha
> >
> >
> >
> > CPPTRAJ: Trajectory Analysis. V16.00
> > ___ ___ ___ ___
> > | \/ | \/ | \/ |
> > _|_/\_|_/\_|_/\_|_
> >
> > | Date/time: 09/27/16 12:28:48
> > | Available memory: 783.544 MB
> >
> > Reading 'input.prmtop' as Amber Topology
> > INPUT: Reading input from 'ptraj.in'
> > [trajin nobadframes.nc]
> > Reading 'nobadframes.nc' as Amber NetCDF
> > Warning: Trajectory box type is 'Orthogonal' but topology box type is
> > 'None'.
> > Warning: Setting topology box information from trajectory.
> > [multidihedral BB phi psi resrange 6-11 out PhiPsi_6-11.dat]
> > MULTIDIHEDRAL: Calculating phi psi dihedrals for residues in range
> 6-11
> > DataSet name: BB
> > Output to PhiPsi_6-11.dat
> > Output range is -180 to 180 degrees.
> > [run]
> > ---------- RUN BEGIN -------------------------------------------------
> >
> > PARAMETER FILES (1 total):
> > 0: input.prmtop, 338 atoms, 25 res, box: Orthogonal, 1 mol
> >
> > INPUT TRAJECTORIES (1 total):
> > 0: 'nobadframes.nc' is a NetCDF AMBER trajectory, Parm input.prmtop
> > (Orthogonal box) (reading 200000 of 200000)
> > Coordinate processing will occur on 200000 frames.
> >
> > BEGIN TRAJECTORY PROCESSING:
> > .....................................................
> > ACTION SETUP FOR PARM 'input.prmtop' (1 actions):
> > 0: [multidihedral BB phi psi resrange 6-11 out PhiPsi_6-11.dat]
> > ResRange=[6-11] phi psi, 12 dihedrals.
> > ----- nobadframes.nc (1-200000, 1) -----
> > 0% 10% Warning: Frame 37873 coords 1 & 2 overlap at origin; may be
> corrupt.
> > Warning: Frame 37878 coords 1 & 2 overlap at origin; may be corrupt.
> > 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
> >
> > Read 200000 frames and processed 200000 frames.
> > TIME: Avg. throughput= 14959.3442 frames / second.
> >
> > ACTION OUTPUT:
> >
> > DATASETS (12 total):
> > BB[phi]:6 "phi:6" (double, torsion(phi)), size is 200000
> > BB[psi]:6 "psi:6" (double, torsion(psi)), size is 200000
> > BB[phi]:7 "phi:7" (double, torsion(phi)), size is 200000
> > BB[psi]:7 "psi:7" (double, torsion(psi)), size is 200000
> > BB[phi]:8 "phi:8" (double, torsion(phi)), size is 200000
> > BB[psi]:8 "psi:8" (double, torsion(psi)), size is 200000
> > BB[phi]:9 "phi:9" (double, torsion(phi)), size is 200000
> > BB[psi]:9 "psi:9" (double, torsion(psi)), size is 200000
> > BB[phi]:10 "phi:10" (double, torsion(phi)), size is 200000
> > BB[psi]:10 "psi:10" (double, torsion(psi)), size is 200000
> > BB[phi]:11 "phi:11" (double, torsion(phi)), size is 200000
> > BB[psi]:11 "psi:11" (double, torsion(psi)), size is 200000
> >
> > DATAFILES (1 total):
> > PhiPsi_6-11.dat (Standard Data File): phi:6 psi:6 phi:7 psi:7 ...
> phi:10
> > psi:10 phi:11 psi:11
> >
> > RUN TIMING:
> > TIME: Init : 0.0000 s ( 0.00%)
> > TIME: Trajectory Process : 13.3696 s ( 82.65%)
> > TIME: Action Post : 0.0000 s ( 0.00%)
> > TIME: Analysis : 0.0000 s ( 0.00%)
> > TIME: Data File Write : 2.8071 s ( 17.35%)
> > TIME: Other : 0.0000 s ( 0.00%)
> > TIME: Run Total 16.1768 s
> > ---------- RUN END ---------------------------------------------------
> > [matrix dihcovar dihedrals BB[*] name DIH out dihcovar.dat]
> > MATRIX: Calculating dihedral covariance matrix, output is by atom.
> > 12 data sets.
> > Printing to file dihcovar.dat
> > Matrix data set is 'DIH'
> > Start: 1 Stop: Final frame
> > [diagmatrix DIH vecs 4 out modes.dihcovar.dat name DIHMODES]
> > Changed DataFile 'modes.dihcovar.dat' type to Evecs file for set
> > DIHMODES
> > DIAGMATRIX: Diagonalizing matrix DIH and writing modes to
> > modes.dihcovar.dat
> > Calculating 4 eigenvectors.
> > Storing modes with name: DIHMODES
> > [run]
> > ---------- RUN BEGIN -------------------------------------------------
> >
> > PARAMETER FILES (1 total):
> > 0: input.prmtop, 338 atoms, 25 res, box: Orthogonal, 1 mol
> >
> > INPUT TRAJECTORIES (1 total):
> > 0: 'nobadframes.nc' is a NetCDF AMBER trajectory, Parm input.prmtop
> > (Orthogonal box) (reading 200000 of 200000)
> > Coordinate processing will occur on 200000 frames.
> >
> > BEGIN TRAJECTORY PROCESSING:
> > .....................................................
> > ACTION SETUP FOR PARM 'input.prmtop' (1 actions):
> > 0: [matrix dihcovar dihedrals BB[*] name DIH out dihcovar.dat]
> > ----- nobadframes.nc (1-200000, 1) -----
> > 0% 10% Warning: Frame 37873 coords 1 & 2 overlap at origin; may be
> corrupt.
> > Warning: Frame 37878 coords 1 & 2 overlap at origin; may be corrupt.
> > 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
> >
> > Read 200000 frames and processed 200000 frames.
> > TIME: Avg. throughput= 88342.5394 frames / second.
> >
> > ACTION OUTPUT:
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > On 23 September 2016 at 22:11, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >
> >> Ah, I see the issue now - you're running the MPI version of cpptraj
> >> and trying to do 2 trajectory processing runs in the same execution
> >> which is currently not supported (and something cpptraj should check
> >> for - details below for those interested). You can still perform the
> >> analysis, you just need to separate it into two runs; one where you
> >> generate the eigenvectors and the second where you project, e.g.
> >>
> >> # Run 1
> >> trajin x.mdcrd
> >> multidihedral BB phi psi resrange 6-11 out PhiPsi_6-11.dat
> >> run
> >> # Calculate dihedral covariance matrix and obtain eigenvectors
> >> matrix dihcovar dihedrals BB[*] out dihcovar.dat name DIH
> >> diagmatrix DIH vecs 4 out modes.dihcovar.dat name DIHMODES
> >> run
> >>
> >>
> >> # Run 2
> >> trajin x.mdcrd
> >> # Read in previously generated dihedral data
> >> readdata PhiPsi_6-11.dat name BB
> >> # Make sure cpptraj knows its dihedral data
> >> dataset mode torsion BB
> >> # Read in previously generated eigenvectors
> >> readdata modes.dihcovar.dat name MyModes
> >> # Project along eigenvectors
> >> projection evecs modes MyModes out dih.project.dat beg 1 end 4
> dihedrals BB
> >> run
> >>
> >> This way should work. Thanks for the report.
> >>
> >> -Dan
> >>
> >> On Thu, Sep 22, 2016 at 10:00 PM, Neha Gandhi <n.gandhiau.gmail.com>
> >> wrote:
> >> > Hi Daniel,
> >> >
> >> > I applied recent patches to AmberTools 16. Here is the output
> >> > CPPTRAJ: Trajectory Analysis. V16.12 MPI
> >> > ___ ___ ___ ___
> >> > | \/ | \/ | \/ |
> >> > _|_/\_|_/\_|_/\_|_
> >> >
> >> > | Running on 6 threads
> >> > | Date/time: 09/23/16 11:53:36
> >> > | Available memory: 21.905 GB
> >> >
> >> > Reading 'input.prmtop' as Amber Topology
> >> > INPUT: Reading input from 'ptraj.in'
> >> > [trajin nobadframes.nc]
> >> > Reading 'nobadframes.nc' as Amber NetCDF
> >> > Warning: Trajectory box type is 'Orthogonal' but topology box type is
> >> > 'None'.
> >> > Warning: Setting topology box information from trajectory.
> >> > [multidihedral BB phi psi resrange 6-11 out PhiPsi_6-11.dat]
> >> > MULTIDIHEDRAL: Calculating phi psi dihedrals for residues in range
> >> 6-11
> >> > DataSet name: BB
> >> > Output to PhiPsi_6-11.dat
> >> > Output range is -180 to 180 degrees.
> >> > [run]
> >> > ---------- RUN BEGIN ------------------------------
> -------------------
> >> >
> >> > PARAMETER FILES (1 total):
> >> > 0: input.prmtop, 338 atoms, 25 res, box: Orthogonal, 1 mol
> >> >
> >> > INPUT TRAJECTORIES (1 total):
> >> > 0: 'nobadframes.nc' is a NetCDF AMBER trajectory, Parm input.prmtop
> >> > (Orthogonal box) (reading 200000 of 200000)
> >> > Coordinate processing will occur on 200000 frames.
> >> >
> >> > PARALLEL INFO:
> >> > Thread 0 will process 33334 frames.
> >> > Thread 1 will process 33334 frames.
> >> > Thread 2 will process 33333 frames.
> >> > Thread 3 will process 33333 frames.
> >> > Thread 4 will process 33333 frames.
> >> > Thread 5 will process 33333 frames.
> >> > .....................................................
> >> > ACTION SETUP FOR PARM 'input.prmtop' (1 actions):
> >> > 0: [multidihedral BB phi psi resrange 6-11 out PhiPsi_6-11.dat]
> >> > ResRange=[6-11] phi psi, 12 dihedrals.
> >> >
> >> > BEGIN PARALLEL TRAJECTORY PROCESSING:
> >> > 0% 10% [1] Warning: Set 37873 coords 1 & 2 overlap at origin; may
> be
> >> > corrupt.
> >> > [1] Warning: Set 37878 coords 1 & 2 overlap at origin; may be
> corrupt.
> >> > 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
> >> > TIME: Rank 0 throughput= 204.0497 frames / second.
> >> > TIME: Rank 1 throughput= 203.6889 frames / second.
> >> > TIME: Rank 2 throughput= 204.1462 frames / second.
> >> > TIME: Rank 3 throughput= 203.3635 frames / second.
> >> > TIME: Rank 4 throughput= 203.6441 frames / second.
> >> > TIME: Rank 5 throughput= 203.7433 frames / second.
> >> > TIME: Avg. throughput= 1220.1928 frames / second.
> >> >
> >> > ACTION OUTPUT:
> >> >
> >> > DATASETS (12 total):
> >> > BB[phi]:6 "phi:6" (double, torsion(phi)), size is 200000
> >> > BB[psi]:6 "psi:6" (double, torsion(psi)), size is 200000
> >> > BB[phi]:7 "phi:7" (double, torsion(phi)), size is 200000
> >> > BB[psi]:7 "psi:7" (double, torsion(psi)), size is 200000
> >> > BB[phi]:8 "phi:8" (double, torsion(phi)), size is 200000
> >> > BB[psi]:8 "psi:8" (double, torsion(psi)), size is 200000
> >> > BB[phi]:9 "phi:9" (double, torsion(phi)), size is 200000
> >> > BB[psi]:9 "psi:9" (double, torsion(psi)), size is 200000
> >> > BB[phi]:10 "phi:10" (double, torsion(phi)), size is 200000
> >> > BB[psi]:10 "psi:10" (double, torsion(psi)), size is 200000
> >> > BB[phi]:11 "phi:11" (double, torsion(phi)), size is 200000
> >> > BB[psi]:11 "psi:11" (double, torsion(psi)), size is 200000
> >> >
> >> > DATAFILES (1 total):
> >> > PhiPsi_6-11.dat (Standard Data File): phi:6 psi:6 phi:7 psi:7 ...
> >> phi:10
> >> > psi:10 phi:11 psi:11
> >> >
> >> > RUN TIMING:
> >> > TIME: Init : 0.0004 s ( 0.00%)
> >> > TIME: Trajectory Process : 163.9085 s ( 80.98%)
> >> > TIME: Data Set Sync : 0.0093 s ( 0.00%)
> >> > TIME: Action Post : 0.0001 s ( 0.00%)
> >> > TIME: Analysis : 0.0000 s ( 0.00%)
> >> > TIME: Data File Write : 38.4950 s ( 19.02%)
> >> > TIME: Other : 0.0002 s ( 0.00%)
> >> > TIME: Run Total 202.4135 s
> >> > ---------- RUN END ------------------------------
> ---------------------
> >> > [matrix dihcovar dihedrals BB[*] name DIH out dihcovar.dat]
> >> > MATRIX: Calculating dihedral covariance matrix, output is by atom.
> >> > 12 data sets.
> >> > Printing to file dihcovar.dat
> >> > Matrix data set is 'DIH'
> >> > Start: 1 Stop: Final frame
> >> > [runanalysis diagmatrix DIH vecs 2 out modes.dihcovar.dat name
> >> DIHMODES]
> >> > Changed DataFile 'modes.dihcovar.dat' type to Evecs file for set
> >> > DIHMODES
> >> > DIAGMATRIX: Diagonalizing matrix DIH and writing modes to
> >> > modes.dihcovar.dat
> >> > Calculating 2 eigenvectors.
> >> > Storing modes with name: DIHMODES
> >> > Eigenmode calculation for 'DIH'
> >> > Warning: Specified # of eigenmodes to calc (2) > matrix dimension (0).
> >> > Warning: Only calculating 0 eigenmodes.
> >> > Calculating eigenvectors and eigenvalues.
> >> > Calculating all eigenmodes.
> >> > ** On entry to DSPEV parameter number 7 had an illegal value
> >> > ** On entry to DSPEV parameter number 7 had an illegal value
> >> > ** On entry to DSPEV parameter number 7 had an illegal value
> >> > ** On entry to DSPEV parameter number 7 had an illegal value
> >> > ** On entry to DSPEV parameter number 7 had an illegal value
> >> >
> >> >
> >> >
> >> >
> >> > On 23 September 2016 at 05:16, Daniel Roe <daniel.r.roe.gmail.com>
> >> wrote:
> >> >
> >> >> Can you post the exact version of cpptraj you are using as well as
> all
> >> >> output? Thanks.
> >> >>
> >> >> -Dan
> >> >>
> >> >> On Wed, Sep 21, 2016 at 11:08 PM, Neha Gandhi <n.gandhiau.gmail.com>
> >> >> wrote:
> >> >> > I am trying to do dihedral PCA and I am following the example in
> >> AMBER16
> >> >> > manual
> >> >> >
> >> >> > trajin x.mdcrd
> >> >> > multidihedral BB phi psi resrange 6-11 out PhiPsi_6-11.dat
> >> >> > run
> >> >> > # Calculate dihedral covariance matrix and obtain eigenvectors
> >> >> > matrix dihcovar dihedrals BB[*] out dihcovar.dat name DIH
> >> >> > diagmatrix DIH vecs 4 out modes.dihcovar.dat name DIHMODES
> >> >> > run
> >> >> > # Project along eigenvectors
> >> >> > projection evecs DIHMODES out dih.project.dat beg 1 end 4 dihedrals
> >> BB[*]
> >> >> > run
> >> >> >
> >> >> >
> >> >> >
> >> >> > I get error-It is not able to read BB[*] data set. I can see that
> the
> >> >> > output file PhiPsi_6-11.dat is not empty.
> >> >> >
> >> >> > Any help is appreciated.
> >> >> >
> >> >> >
> >> >> > --
> >> >> > Regards,
> >> >> > Dr. Neha S. Gandhi,
> >> >> > Vice Chancellor's Research Fellow,
> >> >> > Queensland University of Technology,
> >> >> > 2 George Street, Brisbane, QLD 4000
> >> >> > Australia
> >> >> > LinkedIn
> >> >> > Research Gate
> >> >> > _______________________________________________
> >> >> > AMBER mailing list
> >> >> > AMBER.ambermd.org
> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> -------------------------
> >> >> Daniel R. Roe
> >> >> Laboratory of Computational Biology
> >> >> National Institutes of Health, NHLBI
> >> >> 5635 Fishers Ln, Rm T900
> >> >> Rockville MD, 20852
> >> >> https://www.lobos.nih.gov/lcb
> >> >>
> >> >> _______________________________________________
> >> >> AMBER mailing list
> >> >> AMBER.ambermd.org
> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> >
> >> >
> >> >
> >> > --
> >> > Regards,
> >> > Dr. Neha S. Gandhi,
> >> > Vice Chancellor's Research Fellow,
> >> > Queensland University of Technology,
> >> > 2 George Street, Brisbane, QLD 4000
> >> > Australia
> >> > LinkedIn
> >> > Research Gate
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
> >> --
> >> -------------------------
> >> Daniel R. Roe
> >> Laboratory of Computational Biology
> >> National Institutes of Health, NHLBI
> >> 5635 Fishers Ln, Rm T900
> >> Rockville MD, 20852
> >> https://www.lobos.nih.gov/lcb
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Regards,
> > Dr. Neha S. Gandhi,
> > Vice Chancellor's Research Fellow,
> > Queensland University of Technology,
> > 2 George Street, Brisbane, QLD 4000
> > Australia
> > LinkedIn
> > Research Gate
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Regards,
Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Australia
LinkedIn
Research Gate
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Received on Wed Sep 28 2016 - 03:30:02 PDT
