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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Received on Sat Dec 16 2017 - 06:00:02 PST
