Sir In my laptop i have Trajectory Analysis. V17.00, while on our cluster
we have amber 14 and cpptraj 14.
On Mon, Dec 18, 2017 at 11:58 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> What version of cpptraj is on your laptop and what version is on the
> cluster?
>
> -Dan
>
> On Sat, Dec 16, 2017 at 10:25 AM, Rana Rehan Khalid <rrkhalid.umich.edu>
> wrote:
> > when I did the cpptraj pca analysis on my laptop and run the command one
> by
> > one it works but when i submit my job with the above mentioned script on
> > cluster it show these warnings and job again stop. Thanks
> >
> > [diagmatrix oxxx-covar out oxxx-evecs.dat \ ]
> > Warning: # of eigenvectors specified is < 1 (0) and 'thermo' not
> specified.
> > Warning: Specify # eigenvectors with 'vecs <#>'. Setting to 1.
> > Changed DataFile 'oxxx-evecs.dat' type to Evecs file for set
> > Modes_00004
> > DIAGMATRIX: Diagonalizing matrix oxxx-covar and writing modes to
> > oxxx-evecs.dat
> > Calculating 1 eigenvectors
> > TIME: Total execution time: 230.3207 seconds.
> >
> > On Sat, Dec 16, 2017 at 6:38 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
> > wrote:
> >
> >> Hi sir Thank you. I understand now the point.I change the script as you
> >> guide and ran it works. kindly guide me if any thing wrong in it.
> >>
> >> Regards
> >>
> >> parm ox_solv.prmtop
> >> trajin oxy_1.mdcrd
> >> trajin oxy_2.mdcrd
> >> trajin oxy_3.mdcrd
> >> trajin oxy_4.mdcrd
> >> trajin oxy_5.mdcrd
> >> trajin oxy_6.mdcrd
> >> trajin oxy_7.mdcrd
> >> trajin oxy_8.mdcrd
> >> trajin oxy_10.mdcrd
> >> trajin oxy_11.mdcrd
> >> rms first :1-189&!.H=
> >> average crdset MyAverage
> >> run
> >> rms ref MyAverage :1-189&!.H=
> >> matrix covar name bay1-covar :1-189&!.H=
> >> diagmatrix bay1-covar out bbb-evecs.dat \
> >> vecs 3 name myEvecs \
> >> nmwiz nmwizvecs 3 nmwizfile bbb.nmd nmwizmask :1-189&!.H=
> >> run
> >> rms ref MyAverage :1-189&!.H=
> >> projection HNOX-O2 evecs bbb-evecs.dat myEvecs beg 1 end 3 :1-189&!.H=
> >> crdframes 1,70000
> >> run
> >> hist HNOX-O2:1 bins 100 out oxy-hist.agr norm name OXY-1
> >> hist HNOX-O2:2 bins 100 out oxy-hist.agr norm name OXY-2
> >> hist HNOX-O2:3 bins 100 out oxy-hist.agr norm name OXY-3
> >> run
> >> ##############
> >> clear all
> >> readdata bbb-evecs.dat name Evecs
> >> parm ox_solv.prmtop
> >> parmstrip !(:1-189&!.H=)
> >> parmwrite out oxx-modes.prmtop
> >> runanalysis modes name Evecs trajout oxx-mode1-10.nc \
> >> pcmin -100 pcmax 100 tmode 1 trajoutmask :1-189&!.H= trajoutfmt netcd
> >>
> >> On Sat, Dec 16, 2017 at 1:05 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
> >> wrote:
> >>
> >>> Hi
> >>> I am confused about the <option> I tried to compare it with other PCA
> >>> script and manual to get understanding but not get point. Is it mode
> data
> >>> set like .dat Kindly guide me. Thanks
> >>> diagmatrix bay1-covar name bay1-modes <options>
> >>> modes name bay1-modes <options>
> >>> projection MyProjection evecs bay1-modes <options>
> >>>
> >>> Regards
> >>>
> >>> On Thu, Dec 14, 2017 at 11:21 PM, Daniel Roe <daniel.r.roe.gmail.com>
> >>> wrote:
> >>>
> >>>> Hi,
> >>>>
> >>>> Try doing it without creating a COORDS data set - this stores all your
> >>>> coordinates in memory, which is convenient if you have the memory to
> >>>> spare, but in this case you do not. This means you need to modify your
> >>>> coordinates each time you process them (i.e. you need to rms-fit
> >>>> before you project etc). Something like:
> >>>>
> >>>> # First run to generate average structure
> >>>> trajin bay_1.mdcrd
> >>>> ...
> >>>> rms first <mask>
> >>>> average crdset MyAverage
> >>>> run
> >>>> # Second run to generate covariance matrix and modes. Also run modes
> >>>> analysis.
> >>>> rms ref MyAverage <mask>
> >>>> matrix covar name bay1-covar <mask>
> >>>> diagmatrix bay1-covar name bay1-modes <options>
> >>>> modes name bay1-modes <options>
> >>>> run
> >>>> # Example third run for projection
> >>>> rms ref MyAverage <mask>
> >>>> projection MyProjection evecs bay1-modes <options>
> >>>>
> >>>> Hope this helps,
> >>>>
> >>>> -Dan
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> On Wed, Dec 13, 2017 at 4:58 PM, Rana Rehan Khalid <
> rrkhalid.umich.edu>
> >>>> wrote:
> >>>> > Dear Amber users
> >>>> >
> >>>> > I am trying to run the PCA script every time job stop due to this
> >>>> exceeded
> >>>> > limit of memory
> >>>> >
> >>>> > job 16802098 exceeded MEM usage hard limit (39282 > 2048)
> >>>> >
> >>>> > I use this script for running the job
> >>>> > #!/bin/bash
> >>>> > #PBS -l nodes=1:ppn=1
> >>>> > #PBS -l walltime=100:00:00
> >>>> > cd /nfs/amino-home/rrkhalid/bay60
> >>>> > /nfs/amino-library/local/Amber14/bin/cpptraj -p bay.prmtop -i
> >>>> pca.cpptraj
> >>>> >
> >>>> > and pca.cpptraj script is this each trajectory( 1-10 ) file run
> 750000
> >>>> > steps.
> >>>> > rajin bay_1.mdcrd
> >>>> > trajin bay_2.mdcrd
> >>>> > trajin bay_3.mdcrd
> >>>> > trajin bay_4.mdcrd
> >>>> > trajin bay_5.mdcrd
> >>>> > trajin bay_6.mdcrd
> >>>> > trajin bay_7.mdcrd
> >>>> > trajin bay_8.mdcrd
> >>>> > trajin bay_9.mdcrd
> >>>> > trajin bay_10.mdcrd
> >>>> > rms first :1-189&!.H=
> >>>> > average crdset average
> >>>> > createcrd avgtrajectories
> >>>> > run
> >>>> > crdaction avgtrajectories rms ref average :1-189&!.H=
> >>>> > crdaction avgtrajectories matrix covar name bay1-covar :1-189&!.H=
> >>>> > runanalysis diagmatrix bay1-covar out bay1-evecs.dat \
> >>>> > vecs 3 name myEvecs \
> >>>> > nmwiz nmwizvecs 3 nmwizfile bay.nmd nmwizmask :1-189&!.H=
> >>>> > ##########
> >>>> > clear all
> >>>> > readdata bay1-evecs.dat name Evecs
> >>>> > parm bay.prmtop
> >>>> > parmstrip !(:1-189&!.H=)
> >>>> > parmwrite out bay-modes.prmtop
> >>>> > runanalysis modes name Evecs trajout bay-mode1.nc \
> >>>> > pcmin -100 pcmax 100 tmode 1 trajoutmask :1-189&!.H= trajoutfmt
> netcd
> >>>> >
> >>>> > kindly guide Thanks
> >>>> > _______________________________________________
> >>>> > AMBER mailing list
> >>>> > AMBER.ambermd.org
> >>>> > http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> -------------------------
> >>>> 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
> >>>>
> >>>
> >>>
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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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Received on Mon Dec 18 2017 - 13:30:02 PST
