Thanks Elvis for the reply.
Will do and let you know.
On Mon, Nov 27, 2017 at 5:35 PM, Elvis Martis <elvis.martis.bcp.edu.in>
wrote:
> Hi,
> Still not clear what is wrong.
> I am attaching a script for PCA. Just copy it in the correct directory and
> run "cpptraj -i pca.in" <without quotes.>
> Just tell me if you get the same error.
>
> Best Regards
> Elvis Martis
> Mumbai, INDIA.
>
> ________________________________________
> From: Nisha Amarnath Jonniya <phd1601271002.iiti.ac.in>
> Sent: 27 November 2017 14:15
> To: AMBER Mailing List
> Subject: Re: [AMBER] PCA eigenvalues
>
> Dear Elvis
>
> Though I tried with your comment, but still I got the following error
> after execution of hist command .
> Is it the error with parm.top file??
>
>
> can you help me.
>
>
>
>
> ANALYSIS: Performing 3 analyses:
> 0: [hist ex:1 bins 100 out ex_hist.gnu norm name ex_1]
> Error: HistBin: Max (-16.4714) must be greater than min (-16.4714)
> Error: Could not set up histogram dimension 'ex:1'
> Error: In Analysis [hist]
> 1: [hist ex:2 bins 100 out ex_hist.gnu norm name ex_2]
> Error: HistBin: Max (17.4431) must be greater than min (17.4431)
> Error: Could not set up histogram dimension 'ex:2'
> Error: In Analysis [hist]
> 2: [hist ex:3 bins 100 out ex_hist.gnu norm name ex_3]
> Error: HistBin: Max (-21.5487) must be greater than min (-21.5487)
> Error: Could not set up histogram dimension 'ex:3'
> Error: In Analysis [hist]
>
> TIME: Analyses took 0.0161 seconds.
>
> RUN TIMING:
> TIME: Init : 0.0545 s ( 0.00%)
> TIME: Trajectory Process : 2025.7628 s (100.00%)
> TIME: Action Post : 0.0000 s ( 0.00%)
> TIME: Analysis : 0.0161 s ( 0.00%)
> TIME: Data File Write : 0.0000 s ( 0.00%)
> TIME: Other : 0.0142 s ( 0.00%)
> TIME: Run Total 2025.8477 s
> ---------- RUN END ---------------------------------------------------
> [readdata evececs name Evecs]
> Reading 'evececs' as Evecs file with name 'Evecs'
> Reading modes from evececs
> Warning: DataSet 'Evecs' already present.
> Error: reading datafile evececs
> Error: Could not read data file 'evececs'.
> 1 errors encountered reading input.
> Warning: Set 'ex_1' contains no data.
> Warning: Set 'ex_2' contains no data.
> Warning: Set 'ex_3' contains no data.
> Warning: File 'ex_hist.gnu' has no sets containing data.
> TIME: Total execution time: 8669.3131 seconds.
> Error: Error(s) occurred during execution.
>
>
>
>
>
> On Fri, Nov 24, 2017 at 5:45 PM, Elvis Martis <elvis.martis.bcp.edu.in>
> wrote:
>
> > Hi,
> > Here is the problem
> > "runanalysis diagmatrix ex_covar out evececs 20 name exEvecs:1-273&!.H="
> > Seems like you missed a space there.
> > Try to replace that line with this
> > "runanalysis diagmatrix ex_covar out evececs 20 name ex Evecs
> :1-273&!.H="
> >
> >
> > Best Regards
> > Elvis Martis
> > Mumbai, INDIA.
> >
> > ________________________________________
> > From: Nisha Amarnath Jonniya <phd1601271002.iiti.ac.in>
> > Sent: 24 November 2017 17:09
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] PCA eigenvalues
> >
> > Dear all,
> >
> > As I was also doing PCA analysis. This mail helped me too but I got
> > error in execution of hist: command .
> >
> > These are my script.
> >
> > parm complex_solv.prmtop
> > trajin trajout10-51.mdcrd
> > rms first :1-273&!.H=
> > average crdset ex_average
> > createcrd ex_trajectories
> > run
> > crdaction ex_trajectories rms ref ex_average :1-273&!.H=
> > crdaction ex_trajectories matrix covar name ex_covar :1-273&!.H=
> > runanalysis diagmatrix ex_covar out evececs 20 name exEvecs:1-273&!.H=
> > readdata evececs name Evecs
> > runanalysis modes eigenval name Evecs out evalfrac.dat
> >
> > crdaction ex_trajectories projection ex modes Evecs beg 1 end 3
> > :1-273&!.H= crdframes 84000
> >
> > hist ex:1 bins 100 out 5drb_hist.gnu norm name ex_1
> > hist ex:2 bins 100 out 5drb_hist.gnu norm name ex_2
> > hist ex:3 bins 100 out 5drb_hist.gnu norm name ex_3
> > run
> > readdata evececs name Evecs
> > parm complex_solv.prmtop
> > parmstrip !(:1-273&!.H=)
> > parmwrite out ex_modes.prmtop
> > runanalysis modes name Evecs trajout ex_mode1.nc pcmin -100 pcmax 100
> > tmode
> > 1 trajoutmask :1-273&!.H= trajoutfmt netcdf
> > runanalysis modes name Evecs trajout ex_mode2.nc pcmin -100 pcmax 100
> > tmode
> > 2 trajoutmask :1-273&!.H= trajoutfmt netcdf
> > runanalysis modes name Evecs trajout ex_mode3.nc pcmin -100 pcmax 100
> > tmode
> > 3 trajoutmask :1-273&!.H= trajoutfmt netcdf
> >
> >
> >
> > I am getting error in hist command with following error
> >
> >
> > Data set 'ex:1' not found.
> > Error: Dataset ex:1 not found.
> > Error: Could not setup analysis [hist]
> > 1 errors encountered reading input.
> > Warning: File 'ex_hist.gnu' has no sets containing data.
> >
> >
> >
> >
> > Can you please guide me further how to rectify this problem.
> >
> >
> >
> >
> >
> >
> > On Fri, Nov 24, 2017 at 12:26 AM, Lizelle Lubbe <LBBLIZ002.myuct.ac.za>
> > wrote:
> >
> > > Hi Dan,
> > >
> > > Thanks so much for the great advice you sent earlier.
> > > It worked out well but I noticed the following warning in the output:
> > > Warning: Frame 25 Coordinates out of bounds (100). What does it mean
> and
> > > should I be worried about it?
> > >
> > > The projection of PC1 vs PC2 was written as a gnu file like you
> suggested
> > > and displays a scatter of frames. However, the plot has a black
> > background
> > > and purple dots for each frame which is really not very clear.
> > > Is there any way that I can change the colour or write it in another
> > > format? I can't seem to edit the plot at all in gnuplot.
> > >
> > > Regards
> > >
> > > Lizelle
> > >
> > > ________________________________________
> > > From: Daniel Roe <daniel.r.roe.gmail.com>
> > > Sent: 20 November 2017 05:53:21 PM
> > > To: AMBER Mailing List
> > > Subject: Re: [AMBER] PCA eigenvalues
> > >
> > > s.dat vHi,
> > >
> > > On Sat, Nov 18, 2017 at 10:05 AM, Lizelle Lubbe <LBBLIZ002.myuct.ac.za
> >
> > > wrote:
> > > > Hi Amber users,
> > > >
> > > > I have performed PCA analysis on my MD trajectories in cpptraj and
> > would
> > > like to plot the fraction of total variance vs eigenvalue as shown in
> > > figure s9 of Roe et al 2014 (j phys chem b, 118, 3543-3552).
> > >
> > > To do this you'll want to calculate all principal components (i.e.
> > > eigenvectors) from your covariance matrix, so 3 * the number of
> > > selected atoms. Then you run the 'modes' analysis command with the
> > > 'eigenval' keyword on the resulting modes data, e.g.
> > >
> > > runanalysis diagmatrix myCovar out evececs 246 name myEvecs :1-4&!.H=
> > > runanalysis modes eigenval name myEvecs out evalfrac.dat
> > >
> > > > I also want to have a scatter plot of pc1 vs pc2 and pc2 vs pc3 to
> > > visualize clusters in this space.
> > > > Could someone please guide me in how this can be accomplished?
> > >
> > > For these, just give desired the principal component projection data
> > > set names to the 'hist' command, e.g. for the projection of PC 1 vs 2:
> > >
> > > hist Ndom:1 Ndom:2 bins 100 out Ndom_hist.gnu norm name Ndom_1_2
> > >
> > > > Also, how should the pca histogram analysis be interpreted?
> > >
> > > This is a lot trickier. As you probably know principal components
> > > represent axes that in this case describe variance in the selected
> > > atoms in your system. So PCs can tell you about what the dominant
> > > modes of motion in your system look like, but generally may not tell
> > > you how your system actually moves. Personally I like to visualize the
> > > modes of motion with the 'trajout' keyword of 'modes' (which it
> > > appears you are doing). It can also help to look at the so-called
> > > 'porcupine plots' - I use the nmwiz plugin for VMD (it appears you are
> > > doing that as well).
> > >
> > > Hope this helps,
> > >
> > > -Dan
> > >
> > > >
> > > > This is my pca script:
> > > >
> > > > trajin traj.nc
> > > >
> > > > rms first :1-720&!.H=
> > > >
> > > > average crdset Ndom_average
> > > >
> > > > createcrd Ndom_trajectories
> > > >
> > > > run
> > > >
> > > > crdaction Ndom_trajectories rms ref Ndom_average :1-720&!.H=
> > > >
> > > > crdaction Ndom_trajectories matrix covar name Ndom_covar :1-720&!.H=
> > > >
> > > > runanalysis diagmatrix Ndom_covar out Ndom_evecs.dat vecs 20 name
> > > NdomEvecs nmwiz nmwizvecs 3 nmwizfile Ndom_pca.nmd nmwizmask
> :1-720&!.H=
> > > >
> > > > crdaction Ndom_trajectories projection Ndom modes NdomEvecs beg 1
> end 3
> > > :1-720&!.H= crdframes 1,3000
> > > >
> > > > hist Ndom:1 bins 100 out Ndom_hist.agr norm name Ndom_1
> > > >
> > > > hist Ndom:2 bins 100 out Ndom_hist.agr norm name Ndom_2
> > > >
> > > > hist Ndom:3 bins 100 out Ndom_hist.agr norm name Ndom_3
> > > >
> > > > run
> > > >
> > > > clear all
> > > >
> > > > readdata Ndom_evecs.dat name Evecs
> > > >
> > > > parm NDOM_CPLX_rnb_stripped_box.prmtop
> > > >
> > > > parmstrip !(:1-720&!.H=)
> > > >
> > > > parmwrite out Ndom_modes.prmtop
> > > >
> > > > runanalysis modes name Evecs trajout Ndom_mode1.nc pcmin -100 pcmax
> 100
> > > tmode 1 trajoutmask :1-720&!.H= trajoutfmt netcdf
> > > >
> > > > runanalysis modes name Evecs trajout Ndom_mode2.nc pcmin -100 pcmax
> 100
> > > tmode 2 trajoutmask :1-720&!.H= trajoutfmt netcdf
> > > >
> > > > runanalysis modes name Evecs trajout Ndom_mode3.nc pcmin -100 pcmax
> 100
> > > tmode 3 trajoutmask :1-720&!.H= trajoutfmt netcdf
> > > >
> > > > Kind regards
> > > >
> > > > Lizelle Lubbe
> > > > PhD Chemical Biology candidate
> > > > University of Cape Town
> > > > Disclaimer - University of Cape Town This e-mail is subject to UCT
> > > policies and e-mail disclaimer published on our website at
> > > http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable
> from
> > > +27 21 650 9111. If this e-mail is not related to the business of UCT,
> it
> > > is sent by the sender in an individual capacity. Please report security
> > > incidents or abuse via csirt.uct.ac.za
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> > >
> > >
> > >
> > > --
> > > -------------------------
> > > 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
> > > Disclaimer - University of Cape Town This e-mail is subject to UCT
> > > policies and e-mail disclaimer published on our website at
> > > http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable
> from
> > > +27 21 650 9111. If this e-mail is not related to the business of UCT,
> it
> > > is sent by the sender in an individual capacity. Please report security
> > > incidents or abuse via csirt.uct.ac.za
> > >
> > > _______________________________________________
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> > >
> >
> >
> >
> > --
> >
> > Nisha Amarnath Jonniya
> > PhD Research Scholar
> > Biosciences and Biomedical Engineering
> > Indian Institute of Technology, Indore
> > India
> > _______________________________________________
> > 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
> >
>
>
>
> --
>
> Nisha Amarnath Jonniya
> PhD Research Scholar
> Biosciences and Biomedical Engineering
> Indian Institute of Technology, Indore
> India
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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>
>
--
Nisha Amarnath Jonniya
PhD Research Scholar
Biosciences and Biomedical Engineering
Indian Institute of Technology, Indore
India
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Received on Mon Nov 27 2017 - 04:30:03 PST
