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
>> >>>>
>> >>>
>> >>>
>> >>
>> > _______________________________________________
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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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--
-------------------------
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 Tue Dec 19 2017 - 06:30:05 PST
