On Mon, Aug 3, 2015 at 8:04 AM, George Tzotzos <gtzotzos.me.com> wrote:
> No warnings.
>
> Here’s the output with multihist
> CPPTRAJ: Trajectory Analysis. V13.24
>
Version 13 is a couple of years old at this point. What happens if you use
the most up to date version (15, available as part of AmberTools 15)? You
can also try the version from GitHub: https://github.com/Amber-MD/cpptraj
-Dan
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
> INPUT: Reading Input from file pca.in
> [parm 3n7h_de3_solv.prmtop]
> AmberParm Title: [default_name]
> Radius Set: H(N)-modified Bondi radii (mbondi2)
> [trajin prod_0-20ns.nc]
> [prod_0-20ns.nc] contains 2000 frames.
> [rms first]
> RMSD: (*), reference is first frame (*), with fitting.
> [average avg.nc]
> AVERAGE: Averaging over coordinates in mask [*]
> Start: 1 Stop: Final frame
> Writing averaged coords to [avg.nc]
> [createcrd CRD1]
> CREATECRD: Saving coordinates from Top 3n7h_de3_solv.prmtop to "CRD1"
> [run]
>
> PARAMETER FILES:
> 0: 3n7h_de3_solv.prmtop, 13273 atoms, 3882 res, box: Trunc. Oct., 3758
> mol, 3747 solvent, 2000 frames
>
> INPUT TRAJECTORIES:
> 0: [prod_0-20ns.nc] is a NetCDF AMBER trajectory, Parm
> 3n7h_de3_solv.prmtop (Trunc. Oct. box) (reading 2000 of 2000)
> Coordinate processing will occur on 2000 frames.
>
> REFERENCE COORDS:
> No frames defined.
>
> OUTPUT TRAJECTORIES:
> No files.
>
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> ACTION SETUP FOR PARM [3n7h_de3_solv.prmtop] (3 actions):
> 0: [rms first]
> Mask [*] corresponds to 13273 atoms.
> 1: [average avg.nc]
> AVERAGE: Averaging over 13273 atoms.
> 2: [createcrd CRD1]
> ----- [prod_0-20ns.nc] (1-2000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> Read 2000 frames and processed 2000 frames.
>
> ACTION OUTPUT:
> AVERAGE: [avg.nc ]
> [avg.nc] is a NetCDF AMBER trajectory, Parm 3n7h_de3_solv.prmtop:
> Writing 2000 frames (1-Last, 1)
>
> DATASETS:
> 2 data sets:
> RMSD_00000 "RMSD_00000" (double), size is 2000
> CRD1 "CRD1" (coords), size is 2000 3n7h_de3_solv.prmtop, 13273
> atoms, 3882 res, box: Trunc. Oct., 3758 mol, 3747 solvent
> [reference avg.nc [ref1]]
> [avg.nc] contains 1 frames.
> [avg.nc] is a NetCDF AMBER trajectory, Parm 3n7h_de3_solv.prmtop (reading
> 1 of 1)
> [crdaction CRD1 rms .CA ref [ref1]]
> RMSD: (.CA), reference is reference frame avg.nc (@CA), with fitting.
> Mask [.CA] corresponds to 125 atoms.
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
> [crdaction CRD1 matrix covar name matrixdat @CA out covmat-ca.dat]
> MATRIX: Calculating covar matrix, output is by atom
> Printing to file covmat-ca.dat
> Storing matrix on internal stack with name: matrixdat
> Start: 1 Stop: Final frame
> Mask1: @CA
>
> Mask [.CA] corresponds to 125 atoms.
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
> covmat-ca.dat: Writing 2D data.
> [runanalysis diagmatrix matrixdat out evecs-ca.dat vecs 10 name MyEvecs]
> ANALYZE MATRIX: Analyzing matrix matrixdat and dumping results to
> evecs-ca.dat
> Calculating 10 eigenvectors
> Storing modes with name: MyEvecs
> [run]
>
> PARAMETER FILES:
> 0: 3n7h_de3_solv.prmtop, 13273 atoms, 3882 res, box: Trunc. Oct., 3758
> mol, 3747 solvent, 2000 frames
>
> INPUT TRAJECTORIES:
> 0: [prod_0-20ns.nc] is a NetCDF AMBER trajectory, Parm
> 3n7h_de3_solv.prmtop (Trunc. Oct. box) (reading 2000 of 2000)
> Coordinate processing will occur on 2000 frames.
>
> REFERENCE COORDS:
> The following 1 frames have been defined:
> 0: [ref1] frame 1
> Active reference frame for masks is 0
>
> OUTPUT TRAJECTORIES:
> No files.
>
> BEGIN TRAJECTORY PROCESSING:
> ----- [prod_0-20ns.nc] (1-2000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> Read 2000 frames and processed 2000 frames.
>
> ACTION OUTPUT:
>
> DATASETS:
> 5 data sets:
> RMSD_00000 "RMSD_00000" (double), size is 2000
> CRD1 "CRD1" (coords), size is 2000 3n7h_de3_solv.prmtop, 13273
> atoms, 3882 res, box: Trunc. Oct., 3758 mol, 3747 solvent
> RMSD_00002 "RMSD_00002" (double), size is 2000
> matrixdat "matrixdat" (matrix), size is 70875
> MyEvecs "MyEvecs" (modes), size is 10
> [crdaction CRD1 projection PROJECT modes MyEvecs beg 1 end 2 @CA]
>
> and the output with hist
> INPUT: Reading Input from file pca.in
> [parm 3n7h_de3_solv.prmtop]
> AmberParm Title: [default_name]
> Radius Set: H(N)-modified Bondi radii (mbondi2)
> [trajin prod_0-20ns.nc]
> [prod_0-20ns.nc] contains 2000 frames.
> [rms first]
> RMSD: (*), reference is first frame (*), with fitting.
> [average avg.nc]
> AVERAGE: Averaging over coordinates in mask [*]
> Start: 1 Stop: Final frame
> Writing averaged coords to [avg.nc]
> [createcrd CRD1]
> CREATECRD: Saving coordinates from Top 3n7h_de3_solv.prmtop to "CRD1"
> [run]
>
> PARAMETER FILES:
> 0: 3n7h_de3_solv.prmtop, 13273 atoms, 3882 res, box: Trunc. Oct., 3758
> mol, 3747 solvent, 2000 frames
>
> INPUT TRAJECTORIES:
> 0: [prod_0-20ns.nc] is a NetCDF AMBER trajectory, Parm
> 3n7h_de3_solv.prmtop (Trunc. Oct. box) (reading 2000 of 2000)
> Coordinate processing will occur on 2000 frames.
>
> REFERENCE COORDS:
> No frames defined.
>
> OUTPUT TRAJECTORIES:
> No files.
>
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> ACTION SETUP FOR PARM [3n7h_de3_solv.prmtop] (3 actions):
> 0: [rms first]
> Mask [*] corresponds to 13273 atoms.
> 1: [average avg.nc]
> AVERAGE: Averaging over 13273 atoms.
> 2: [createcrd CRD1]
> ----- [prod_0-20ns.nc] (1-2000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> Read 2000 frames and processed 2000 frames.
>
> ACTION OUTPUT:
> AVERAGE: [avg.nc ]
> [avg.nc] is a NetCDF AMBER trajectory, Parm 3n7h_de3_solv.prmtop:
> Writing 2000 frames (1-Last, 1)
>
> DATASETS:
> 2 data sets:
> RMSD_00000 "RMSD_00000" (double), size is 2000
> CRD1 "CRD1" (coords), size is 2000 3n7h_de3_solv.prmtop, 13273
> atoms, 3882 res, box: Trunc. Oct., 3758 mol, 3747 solvent
> [reference avg.nc [ref1]]
> [avg.nc] contains 1 frames.
> [avg.nc] is a NetCDF AMBER trajectory, Parm 3n7h_de3_solv.prmtop (reading
> 1 of 1)
> [crdaction CRD1 rms @CA ref [ref1]]
> RMSD: (.CA), reference is reference frame avg.nc (@CA), with fitting.
> Mask [@CA] corresponds to 125 atoms.
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
> [crdaction CRD1 matrix covar name matrixdat @CA out covmat-ca.dat]
> MATRIX: Calculating covar matrix, output is by atom
> Printing to file covmat-ca.dat
> Storing matrix on internal stack with name: matrixdat
> Start: 1 Stop: Final frame
> Mask1: .CA
>
> Mask [@CA] corresponds to 125 atoms.
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
> covmat-ca.dat: Writing 2D data.
> [runanalysis diagmatrix matrixdat out evecs-ca.dat vecs 10 name MyEvecs]
> ANALYZE MATRIX: Analyzing matrix matrixdat and dumping results to
> evecs-ca.dat
> Calculating 10 eigenvectors
> Storing modes with name: MyEvecs
> [run]
>
> PARAMETER FILES:
> 0: 3n7h_de3_solv.prmtop, 13273 atoms, 3882 res, box: Trunc. Oct., 3758
> mol, 3747 solvent, 2000 frames
>
> INPUT TRAJECTORIES:
> 0: [prod_0-20ns.nc] is a NetCDF AMBER trajectory, Parm
> 3n7h_de3_solv.prmtop (Trunc. Oct. box) (reading 2000 of 2000)
> Coordinate processing will occur on 2000 frames.
>
> REFERENCE COORDS:
> The following 1 frames have been defined:
> 0: [ref1] frame 1
> Active reference frame for masks is 0
>
> OUTPUT TRAJECTORIES:
> No files.
>
> BEGIN TRAJECTORY PROCESSING:
> ----- [prod_0-20ns.nc] (1-2000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> Read 2000 frames and processed 2000 frames.
>
> ACTION OUTPUT:
>
> DATASETS:
> 5 data sets:
> RMSD_00000 "RMSD_00000" (double), size is 2000
> CRD1 "CRD1" (coords), size is 2000 3n7h_de3_solv.prmtop, 13273
> atoms, 3882 res, box: Trunc. Oct., 3758 mol, 3747 solvent
> RMSD_00002 "RMSD_00002" (double), size is 2000
> matrixdat "matrixdat" (matrix), size is 70875
> MyEvecs "MyEvecs" (modes), size is 10
> [crdaction CRD1 projection PROJECT modes MyEvecs beg 1 end 2 @CA]
>
> > On 3 Aug 2015, at 17:01, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> >
> >>
> >>
> >> RMSD_00002 "RMSD_00002" (double), size is 2000
> >> matrixdat "matrixdat" (matrix), size is 70875
> >> MyEvecs "MyEvecs" (modes), size is 10
> >> [crdaction CRD1 projection PROJECT modes MyEvecs beg 1 end 2 @CA]
> >>
> >
> > I really need to see the entire output. If this is where your calculation
> > stops then clearly something is wrong because the histogram command isn't
> > even attempted. Are you certain you don't get any 'Warning:' or 'Error:'
> > messages? Also what version of cpptraj is this? (cpptraj --version)
> >
> > -Dan
> >
> >
> >>
> >>
> >> Running hist and generating a gnu output file also fails to generate a
> >> histogram
> >>
> >> runanalysis hist PROJECT:1 PROJECT:2 free 300 out fhist-all.CA.gnu bins
> >> 400
> >>
> >> has the same effect. Same files generated but no histogram
> >>
> >> Regards
> >>
> >> George
> >>
> >>
> >>> On 3 Aug 2015, at 16:14, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> >>>
> >>> Hi,
> >>>
> >>> Were there any Warning or Error messages printed by cpptraj? I think
> the
> >>> problem here is you are creating a 2D histogram with 'hist' but writing
> >> to
> >>> a format that doesn't support 2D writes (agr). Try a different output
> >>> format (like gnu) or use 'multihist' to create two 1D histograms.
> >>>
> >>> -Dan
> >>>
> >>> On Mon, Aug 3, 2015 at 4:46 AM, George Tzotzos <gtzotzos.me.com>
> wrote:
> >>>
> >>>> I’m trying to conduct a PCA analysis of a trajectory, based on earlier
> >>>> suggestions from the amber list (10 March 2015).
> >>>>
> >>>> Below is the script that I used. It seems to run as expected or almost
> >> as
> >>>> expected because it fails to generate the histogram as given in the
> last
> >>>> line of the input script.
> >>>>
> >>>> I’d be grateful for any suggestions dealing with this problem.
> >>>>
> >>>> Regards
> >>>>
> >>>> George
> >>>>
> >>>>
> >>>> parm 3n7h_de3_solv.prmtop
> >>>> trajin prod_0-20ns.nc
> >>>> rms first
> >>>> average avg.nc
> >>>> createcrd CRD1
> >>>> run
> >>>> reference avg.nc [ref1]
> >>>> crdaction CRD1 rms .CA ref [ref1]
> >>>> crdaction CRD1 matrix covar name matrixdat @CA out covmat-ca.dat
> >>>> runanalysis diagmatrix matrixdat out evecs-ca.dat vecs 10 name MyEvecs
> >>>> run
> >>>> crdaction CRD1 projection PROJECT modes MyEvecs beg 1 end 2 @CA
> >>>> runanalysis hist PROJECT:1 PROJECT:2 free 300 out fhist-all.CA.agr
> bins
> >>>> 400
> >>>> _______________________________________________
> >>>> 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 307
> >>> 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 <mailto:AMBER.ambermd.org>
> >> http://lists.ambermd.org/mailman/listinfo/amber <
> http://lists.ambermd.org/mailman/listinfo/amber>
> >>
> >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Department of Medicinal Chemistry
> > University of Utah
> > 30 South 2000 East, Room 307
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/ <
> http://home.chpc.utah.edu/~cheatham/>
> > (801) 587-9652
> > (801) 585-6208 (Fax)
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org <mailto:AMBER.ambermd.org>
> > http://lists.ambermd.org/mailman/listinfo/amber <
> 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 307
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
Received on Mon Aug 03 2015 - 08:00:04 PDT
