Yes sir It works now thank you.
On Tue, Dec 19, 2017 at 7:23 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> You should upgrade to AmberTools 17 on your cluster.
>
> -Dan
>
> On Mon, Dec 18, 2017 at 4:16 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
> wrote:
> > 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
> >>
> >> _______________________________________________
> >> 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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>
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Received on Tue Dec 19 2017 - 06:30:06 PST
