No warnings.
Here’s the output with multihist
CPPTRAJ: Trajectory Analysis. V13.24
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
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>
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Received on Mon Aug 03 2015 - 07:30:03 PDT
