Hi,
Ah, I see what's going on now. You are putting the 'hist' commands in
the analysis list, which sets up the output data sets and data file
but does not execute it. Then you are running the 'modes' analysis
immediately with 'runanalysis'. At that point the 'hist' commands are
in the analysis list, but since they have not been run the histogram
data has not been generated, which is why you receive those warnings.
Once the 'hist' commands are executed the data is generated and all is
well. If you wanted to get rid of those warnings in your output just
remove 'runanalysis' from before the 'modes' command so that 'modes'
goes into the analysis list as well. Then change your 'run' at the end
to 'runanalysis' with no other arguments, which means "execute all
analyses in the analysis list without reading through the trajectory
again", e.g.:
hist myproj:1,*,*,*,200 out pca1.hist.agr normint name PC-1
...
hist myproj:7,*,*,*,200 out pca1.hist.agr normint name PC-7
modes name evecs1.dat trajout pc1.pdb trajoutfmt pdb trajoutmask
:1-164&!.H= pcmin -100 pcmax 100 tmode 1
runanalysis
-Dan
On Tue, Aug 12, 2014 at 1:17 PM, Jonathan Gough
<jonathan.d.gough.gmail.com> wrote:
> 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)
>>
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>>
> _______________________________________________
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--
-------------------------
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)
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Received on Tue Aug 12 2014 - 13:00:03 PDT
