Amber versions:
[jonathan.mdbox3 dimer-2KLR]$ /home/jonathan/amber14/update_amber -v
Version is reported as <version>.<patches applied>
AmberTools version 14.07
Amber version 14.03
[jonathan.mdbox3 dimer-2KLR]$
REVISED CPPTRAJ SCRIPT:
parm nowat.dimer-2KLR.prmtop
trajin prod01.nc
rms first :1-164&!.H= out prod01.rmsd
average dimerAVG.rst restart
createcrd crd1
run
reference dimerAVG.rst.1 [avg]
crdaction crd1 rms ref [avg] :1-164&!.H=
crdaction crd1 matrix covar :1-164&!.H= name dimerCovar
runanalysis diagmatrix dimerCovar out evecs1.dat vecs 10 name evecs1.dat
crdaction crd1 projection modes evecs1.dat beg 1 end 10 :1-164&!.H= myproj
hist myproj:1,*,*,*,200 out pca1.hist.agr normint name PC-1
hist myproj:2,*,*,*,200 out pca1.hist.agr normint name PC-2
hist myproj:3,*,*,*,200 out pca1.hist.agr normint name PC-3
hist myproj:4,*,*,*,200 out pca1.hist.agr normint name PC-4
hist myproj:5,*,*,*,200 out pca1.hist.agr normint name PC-5
hist myproj:6,*,*,*,200 out pca1.hist.agr normint name PC-6
hist myproj:7,*,*,*,200 out pca1.hist.agr normint name PC-7
runanalysis modes name evecs1.dat trajout pc1.pdb trajoutfmt pdb
trajoutmask :1-164&!.H= pcmin -100 pcmax 100 tmode 1
run
quit
[jonathan.mdbox3 dimer-2KLR]$ cpptraj -i newpc3.ptraj
CPPTRAJ: Trajectory Analysis. V14.05
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
INPUT: Reading Input from file newpc3.ptraj
[parm nowat.dimer-2KLR.prmtop]
Reading 'nowat.dimer-2KLR.prmtop' as Amber Topology
[trajin prod01.nc]
Reading 'prod01.nc' as Amber NetCDF
[rms first :1-164&!.H= out prod01.rmsd]
RMSD: (:1-164&!.H*), reference is first frame (:1-164&!.H*), with
fitting.
[average dimerAVG.rst restart]
AVERAGE: Averaging over coordinates in mask [*]
Start: 1 Stop: Final frame
Writing averaged coords to [dimerAVG.rst]
[createcrd crd1]
CREATECRD: Saving coordinates from Top nowat.dimer-2KLR.prmtop to "crd1"
[run]
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES:
0: 'nowat.dimer-2KLR.prmtop', 2666 atoms, 164 res, box: Trunc. Oct., 2
mol, 5000 frames
INPUT TRAJECTORIES:
0: 'prod01.nc' is a NetCDF AMBER trajectory, Parm nowat.dimer-2KLR.prmtop
(Trunc. Oct. box) (reading 5000 of 5000)
Coordinate processing will occur on 5000 frames.
TIME: Run Initialization took 0.0000 seconds.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'nowat.dimer-2KLR.prmtop' (3 actions):
0: [rms first :1-164&!.H= out prod01.rmsd]
Mask [:1-164&!.H*] corresponds to 1334 atoms.
Mask [:1-164&!.H*] corresponds to 1334 atoms.
Warning: Coordinates are being rotated and box coordinates are present.
Warning: Unit cell vectors are NOT rotated; imaging will not be possible
Warning: after the RMS-fit is performed.
1: [average dimerAVG.rst restart]
Averaging over 2666 atoms.
2: [createcrd crd1]
----- prod01.nc (1-5000, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 5000 frames and processed 5000 frames.
TIME: Trajectory processing: 0.7454 s
TIME: Avg. throughput= 6708.0329 frames / second.
ACTION OUTPUT:
AVERAGE: [dimerAVG.rst restart]
Writing 'dimerAVG.rst' as Amber Restart
'dimerAVG.rst' is an AMBER restart file, Parm nowat.dimer-2KLR.prmtop:
Writing 5000 frames (1-Last, 1)
DATASETS:
2 data sets:
RMSD_00000 "RMSD_00000" (double, rms), size is 5000
crd1 "crd1" (coordinates), size is 5000 (152 MB) Box Coords, 2666 atoms
DATAFILES:
prod01.rmsd (Standard Data File): RMSD_00000
---------- RUN END ---------------------------------------------------
[reference dimerAVG.rst.1 [avg]]
Reading 'dimerAVG.rst.1' as Amber Restart
'dimerAVG.rst.1' is an AMBER restart file, no velocities, Parm
nowat.dimer-2KLR.prmtop (reading 1 of 1)
[crdaction crd1 rms ref [avg] :1-164&!.H=]
Mask [:1-164&!.H*] corresponds to 1334 atoms.
RMSD: (:1-164&!.H*), reference is reference frame dimerAVG.rst.1
(:1-164&!.H*), with fitting.
Mask [:1-164&!.H*] corresponds to 1334 atoms.
Warning: Coordinates are being rotated and box coordinates are present.
Warning: Unit cell vectors are NOT rotated; imaging will not be possible
Warning: after the RMS-fit is performed.
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
TIME: Total action execution time: 0.3793 seconds.
[crdaction crd1 matrix covar :1-164&!.H= name dimerCovar]
MATRIX: Calculating covariance matrix, output is by atom
Storing matrix on internal stack with name: dimerCovar
Start: 1 Stop: Final frame
Mask1: :1-164&!.H*
Mask [:1-164&!.H*] corresponds to 1334 atoms.
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
TIME: Total action execution time: 60.4692 seconds.
[runanalysis diagmatrix dimerCovar out evecs1.dat vecs 10 name evecs1.dat]
Changed DataFile 'evecs1.dat' type to Evecs file for set evecs1.dat
DIAGMATRIX: Diagonalizing matrix dimerCovar and writing modes to
evecs1.dat
Calculating 10 eigenvectors
Storing modes with name: evecs1.dat
TIME: Total analysis execution time: 1.4651 seconds.
[crdaction crd1 projection modes evecs1.dat beg 1 end 10 :1-164&!.H=
myproj]
PROJECTION: Calculating projection using eigenvectors 1 to 10 of
evecs1.dat
Start: 1 Stop: Final frame
Atom Mask: [:1-164&!.H*]
Mask [:1-164&!.H*] corresponds to 1334 atoms.
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
TIME: Total action execution time: 0.5037 seconds.
[hist myproj:1,*,*,*,200 out pca1.hist.agr normint name PC-1]
Hist: pca1.hist.agr: Set up for 1 dimensions using the following datasets:
[ Mode1 ]
normint: Integral over bins will be normalized to 1.0.
[hist myproj:2,*,*,*,200 out pca1.hist.agr normint name PC-2]
Hist: pca1.hist.agr: Set up for 1 dimensions using the following datasets:
[ Mode2 ]
normint: Integral over bins will be normalized to 1.0.
[hist myproj:3,*,*,*,200 out pca1.hist.agr normint name PC-3]
Hist: pca1.hist.agr: Set up for 1 dimensions using the following datasets:
[ Mode3 ]
normint: Integral over bins will be normalized to 1.0.
[hist myproj:4,*,*,*,200 out pca1.hist.agr normint name PC-4]
Hist: pca1.hist.agr: Set up for 1 dimensions using the following datasets:
[ Mode4 ]
normint: Integral over bins will be normalized to 1.0.
[hist myproj:5,*,*,*,200 out pca1.hist.agr normint name PC-5]
Hist: pca1.hist.agr: Set up for 1 dimensions using the following datasets:
[ Mode5 ]
normint: Integral over bins will be normalized to 1.0.
[hist myproj:6,*,*,*,200 out pca1.hist.agr normint name PC-6]
Hist: pca1.hist.agr: Set up for 1 dimensions using the following datasets:
[ Mode6 ]
normint: Integral over bins will be normalized to 1.0.
[hist myproj:7,*,*,*,200 out pca1.hist.agr normint name PC-7]
Hist: pca1.hist.agr: Set up for 1 dimensions using the following datasets:
[ Mode7 ]
normint: Integral over bins will be normalized to 1.0.
[runanalysis modes name evecs1.dat trajout pc1.pdb trajoutfmt pdb
trajoutmask :1-164&!.H= pcmin -100 pcmax 100 tmode 1]
Mask [:1-164&!.H*] corresponds to 1334 atoms.
Writing 'pc1.pdb' as PDB
ANALYZE MODES: Calculating coordinate projection using modes from
evecs1.dat
Creating trajectory for mode 1
Writing to trajectory pc1.pdb
PC range: -100.000000 to 100.000000
Warning: Set 'PC-1' contains no data.
Warning: Set 'PC-2' contains no data.
Warning: Set 'PC-3' contains no data.
Warning: Set 'PC-4' contains no data.
Warning: Set 'PC-5' contains no data.
Warning: Set 'PC-6' contains no data.
Warning: Set 'PC-7' contains no data.
Warning: File 'pca1.hist.agr' has no sets containing data.
TIME: Total analysis execution time: 0.7967 seconds.
[run]
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES:
0: 'nowat.dimer-2KLR.prmtop', 2666 atoms, 164 res, box: Trunc. Oct., 2
mol, 5000 frames
INPUT TRAJECTORIES:
0: 'prod01.nc' is a NetCDF AMBER trajectory, Parm nowat.dimer-2KLR.prmtop
(Trunc. Oct. box) (reading 5000 of 5000)
Coordinate processing will occur on 5000 frames.
REFERENCE FRAMES (1 total):
0: [avg] 'dimerAVG.rst.1', frame 1
Active reference frame for masks is 0
TIME: Run Initialization took 0.0000 seconds.
BEGIN TRAJECTORY PROCESSING:
----- prod01.nc (1-5000, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 5000 frames and processed 5000 frames.
TIME: Trajectory processing: 0.2767 s
TIME: Avg. throughput= 18069.5243 frames / second.
ACTION OUTPUT:
ANALYSIS: Performing 7 analyses:
0: [hist myproj:1,*,*,*,200 out pca1.hist.agr normint name PC-1]
Dim myproj:1: -99.079651->85.474983, step 0.922773, 200 bins.
Hist: 5000 data points in each dimension.
Hist: Allocating histogram, total bins = 200
Warning: Frame 2259 Coordinates out of bounds (200)
Histogram: Normalizing integral over bin populations to 1.0
Sum over all bins is 4999.000000
1: [hist myproj:2,*,*,*,200 out pca1.hist.agr normint name PC-2]
Dim myproj:2: -58.574547->52.875103, step 0.557248, 200 bins.
Hist: 5000 data points in each dimension.
Hist: Allocating histogram, total bins = 200
Warning: Frame 2195 Coordinates out of bounds (200)
Histogram: Normalizing integral over bin populations to 1.0
Sum over all bins is 4999.000000
2: [hist myproj:3,*,*,*,200 out pca1.hist.agr normint name PC-3]
Dim myproj:3: -47.821564->60.409298, step 0.541154, 200 bins.
Hist: 5000 data points in each dimension.
Hist: Allocating histogram, total bins = 200
Histogram: Normalizing integral over bin populations to 1.0
Sum over all bins is 5000.000000
3: [hist myproj:4,*,*,*,200 out pca1.hist.agr normint name PC-4]
Dim myproj:4: -30.283112->39.925571, step 0.351043, 200 bins.
Hist: 5000 data points in each dimension.
Hist: Allocating histogram, total bins = 200
Warning: Frame 1588 Coordinates out of bounds (200)
Histogram: Normalizing integral over bin populations to 1.0
Sum over all bins is 4999.000000
4: [hist myproj:5,*,*,*,200 out pca1.hist.agr normint name PC-5]
Dim myproj:5: -23.813276->24.682325, step 0.242478, 200 bins.
Hist: 5000 data points in each dimension.
Hist: Allocating histogram, total bins = 200
Warning: Frame 3108 Coordinates out of bounds (200)
Histogram: Normalizing integral over bin populations to 1.0
Sum over all bins is 4999.000000
5: [hist myproj:6,*,*,*,200 out pca1.hist.agr normint name PC-6]
Dim myproj:6: -29.690786->31.783808, step 0.307373, 200 bins.
Hist: 5000 data points in each dimension.
Hist: Allocating histogram, total bins = 200
Warning: Frame 213 Coordinates out of bounds (200)
Histogram: Normalizing integral over bin populations to 1.0
Sum over all bins is 4999.000000
6: [hist myproj:7,*,*,*,200 out pca1.hist.agr normint name PC-7]
Dim myproj:7: -27.663399->32.142406, step 0.299029, 200 bins.
Hist: 5000 data points in each dimension.
Hist: Allocating histogram, total bins = 200
Warning: Frame 1759 Coordinates out of bounds (200)
Histogram: Normalizing integral over bin populations to 1.0
Sum over all bins is 4999.000000
TIME: Analyses took 0.0011 seconds.
DATASETS:
22 data sets:
RMSD_00000 "RMSD_00000" (double, rms), size is 5000
crd1 "crd1" (coordinates), size is 5000 (152 MB) Box Coords, 2666 atoms
RMSD_00002 "RMSD_00002" (double, rms), size is 5000
dimerCovar "dimerCovar" (double matrix), size is 8010003
evecs1.dat "evecs1.dat" (eigenmodes), size is 10
myproj:1 "Mode1" (float), size is 5000
myproj:2 "Mode2" (float), size is 5000
myproj:3 "Mode3" (float), size is 5000
myproj:4 "Mode4" (float), size is 5000
myproj:5 "Mode5" (float), size is 5000
myproj:6 "Mode6" (float), size is 5000
myproj:7 "Mode7" (float), size is 5000
myproj:8 "Mode8" (float), size is 5000
myproj:9 "Mode9" (float), size is 5000
myproj:10 "Mode10" (float), size is 5000
PC-1 "PC-1" (double), size is 200
PC-2 "PC-2" (double), size is 200
PC-3 "PC-3" (double), size is 200
PC-4 "PC-4" (double), size is 200
PC-5 "PC-5" (double), size is 200
PC-6 "PC-6" (double), size is 200
PC-7 "PC-7" (double), size is 200
DATAFILES:
prod01.rmsd (Standard Data File): RMSD_00000
evecs1.dat (Evecs file): evecs1.dat
pca1.hist.agr (Grace File): PC-1 PC-2 PC-3 PC-4 PC-5 PC-6 PC-7
---------- RUN END ---------------------------------------------------
[quit]
TIME: Total execution time: 64.6683 seconds.
--------------------------------------------------------------------------------
To cite CPPTRAJ use:
Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
Theory Comput., 2013, 9 (7), pp 3084-3095.
[jonathan.mdbox3 dimer-2KLR]$
On Tue, Aug 12, 2014 at 3:06 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Tue, Aug 12, 2014 at 11:47 AM, Jonathan Gough
> <jonathan.d.gough.gmail.com> wrote:
> > 1. I would like to simply calculate the the first 20 PC and plot their
> > respective histograms for the entire trajectory (Is this appropriate or
> am
> > i supposed to break things up as you did in the paper?). Below is the
> > cpptraj script.
>
> That's fine, although you need to keep your mask consistent, so in the
> 'modes' command change to 'trajoutmask :1-164&!.H='. The only reason I
> calculated the eigenvectors using the combined trajectory was to
> ensure that all principal components would be the same for each
> individual trajectory. By subsequently calculating the projections on
> the individual trajectories you can then essentially see that
> trajectory's contribution to the PC.
>
> > I tried doing this but I get an error saying that:
> >
> > "Warning: Set 'PC-1' contains no data" and indeed no histograms are
> > produced... where am I going wrong?
>
> This is strange. Are you sure you are using an up-to-date version of
> cpptraj? Older versions of the 'hist' analysis did not use the 'name'
> keyword. I would need to see your entire cpptraj output to debug
> further.
>
> > 2. We would like to visualize the trajectory of the PC. Using the modes
> > (analyze modes) command, (section 28.14.3) we can spit out a trajectory
> > (trajout). That being said... there isn't a prmtop for the output file.
>
> You can easily create a topology to match your trajectory using
> 'parmstrip'/'parmwrite', e.g.
>
> parm nowat.dimer.prmtop
> parmstrip !(:1-164&!.H=)
> parmwrite out modes.parm7
>
>
> Hope this helps,
>
> -Dan
>
> >
> > Is there a way to generate a prmtop for said trajectory?
> >
> > If it's done as a pdb, It does spit out something that is viewable, but
> > there aren't any TER cards or frame end statements between the different
> > models, therefore whatever is "visualized" is a horrendous mess.
> > What is the best way to output models that can be visualized?
> > Is there a way to output specific frames with all atoms?
> >
> > Any help would be appreciated!
> > Jonathan
> >
> > cpptraj script:
> > parm nowat.dimer.prmtop
> > trajin prod01.nc
> > rms first :1-164&!.H=
> > average dimerAVG.rst restart
> > createcrd crd1
> > run
> > reference dimerAVG.rst.1 [avg]
> > crdaction crd1 rms ref [avg] :1-164&!.H=
> > crdaction crd1 matrix covar :1-164&!.H= name dimerCovar
> > runanalysis diagmatrix dimerCovar out evecs1.dat vecs 20 name evecs1.dat
> > crdaction crd1 projection modes evecs1.dat beg 1 end 20 :1-164&!.H=
> myproj
> > hist myproj:1 bins 200 out pca1.hist.agr normint name PC-1
> > hist myproj:2 bins 200 out pca1.hist.agr normint name PC-2
> > hist myproj:3 bins 200 out pca1.hist.agr normint name PC-3
> > hist myproj:4 bins 200 out pca1.hist.agr normint name PC-4
> > hist myproj:5 bins 200 out pca1.hist.agr normint name PC-5
> > hist myproj:6 bins 200 out pca1.hist.agr normint name PC-6
> > hist myproj:7 bins 200 out pca1.hist.agr normint name PC-7
> > runanalysis modes name evecs1.dat trajout pc1.pdb trajoutfmt pdb
> > trajoutmask :1-164 tmode 1
> > run
> > quit
> >
> >
> >
> >
> > On Fri, Aug 8, 2014 at 12:41 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >
> >> Hi,
> >>
> >> Add 'name evecs.dat' to the 'runanalysis diagmatrix' line. This will
> >> name the modes data set created by diagmatrix to 'evecs.dat' so that
> >> the subsequent 'projection' commands can find it, e.g.:
> >>
> >> runanalysis diagmatrix dimerCovar out evecs.dat vecs 20 name evecs.dat
> >>
> >> Let me know if that doesn't work for you,
> >>
> >> -Dan
> >>
> >> On Fri, Aug 8, 2014 at 10:17 AM, Jonathan Gough
> >> <jonathan.d.gough.gmail.com> wrote:
> >> > Hi,
> >> >
> >> > I am attempting to use the cpptraj script described in the paper:
> >> >
> >> > "Evaluation of Enhanced Sampling Provided by Accelerated
> >> > Molecular Dynamics with Hamiltonian Replica Exchange Methods
> >> > Daniel R. Roe, Christina Bergonzo, and Thomas E. Cheatham, III"
> >> >
> >> > I am essentially using the same script as described in the
> supplemental
> >> > info, modified for my system.
> >> >
> >> > I believe the script is getting stuck at the command:
> >> > crdaction crd1 projection T1 modes evecs.dat beg 1 end 20
> >> :1-164&!.N,CA,C= \
> >> > crdframes 568,10566 out T1.dat
> >> >
> >> > Stating that " Error: Modes should be read in prior to this command
> with
> >> > 'readdata' "
> >> >
> >> > That being said, I am not sure where said modes are to be called
> from. I
> >> > thought those were generated by the ccptraj script.
> >> >
> >> > ANy insight would be appreciated.
> >> >
> >> > note: running
> >> > AmberTools version 14.07
> >> > Amber version 14.03
> >> >
> >> > here is the script I am using:
> >> >
> >> > parm dimer.prmtop
> >> > trajin prod01-dimer.mdcrd
> >> > trajin prod02-dimer.mdcrd
> >> > trajin prod03-dimer.mdcrd
> >> > trajin prod04-dimer.mdcrd
> >> > autoimage
> >> > rms first :1-164&!.N,CA,C=
> >> > average dimerAVG.rst restart
> >> > createcrd crd1
> >> > run
> >> > reference dimerAVG.rst.1 [avg]
> >> > crdaction crd1 rms ref [avg] :1-164&!.N,CA,C=
> >> > crdaction crd1 matrix covar :1-164&!.N,CA,C= name dimerCovar
> >> > runanalysis diagmatrix dimerCovar out evecs.dat vecs 20
> >> > crdaction crd1 projection T1 modes evecs.dat beg 1 end 20
> >> :1-164&!.N,CA,C= \
> >> > crdframes 568,10566 out T1.dat
> >> > crdaction crd1 projection T2 modes evecs.dat beg 1 end 20
> >> :1-164&!.N,CA,C= \
> >> > crdframes 10568,20566 out T2.dat
> >> > crdaction crd1 projection T3 modes evecs.dat beg 1 end 20
> >> :1-164&!.N,CA,C= \
> >> > crdframes 20568,30566 out T3.dat
> >> > crdaction crd1 projection T4 modes evecs.dat beg 1 end 20
> >> :1-164&!.N,CA,C= \
> >> > crdframes 30568,40566 out T4.dat
> >> > kde T1:1 kldiv T2:1 klout KL-PC.agr bins 400 name MD-1
> >> > kde T1:2 kldiv T2:2 klout KL-PC.agr bins 400 name MD-2
> >> > kde T1:3 kldiv T2:3 klout KL-PC.agr bins 400 name MD-3
> >> > kde T1:4 kldiv T2:4 klout KL-PC.agr bins 400 name MD-4
> >> > kde T1:1 out kde-PC.agr bins 400 name KDE1-1
> >> > kde T1:2 out kde-PC.agr bins 400 name KDE1-2
> >> > hist T1:1,*,*,*,200 out pca.hist.agr normint name HIST1-1
> >> > hist T2:1,*,*,*,200 out pca.hist.agr normint name HIST1-2
> >> > run
> >> > quit
> >> > _______________________________________________
> >> > 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
> > 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
>
_______________________________________________
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Received on Tue Aug 12 2014 - 12:30:03 PDT
