Dear,
I got the result for PCA.
As I am new to this, I could not able to analyze the result.
Can you help me. I am attaching my plot.
On Mon, Nov 27, 2017 at 5:50 PM, Nisha Amarnath Jonniya <
phd1601271002.iiti.ac.in> wrote:
> 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
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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
>> > >
>> > > _______________________________________________
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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
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>>
>>
>> --
>>
>> Nisha Amarnath Jonniya
>> PhD Research Scholar
>> Biosciences and Biomedical Engineering
>> Indian Institute of Technology, Indore
>> India
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>
>
> --
>
> Nisha Amarnath Jonniya
> PhD Research Scholar
> Biosciences and Biomedical Engineering
> Indian Institute of Technology, Indore
> India
>
>
--
Nisha Amarnath Jonniya
PhD Research Scholar
Biosciences and Biomedical Engineering
Indian Institute of Technology, Indore
India
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Received on Tue Nov 28 2017 - 01:00:03 PST
