[AMBER] pca - Projecting vectors onto a trajectory

From: Prasanth G, Research Scholar <prasanthghanta.sssihl.edu.in>
Date: Thu, 18 Jul 2019 16:10:34 +0530

Dear all,

I am interested in projecting the vectors of the protein in water over a
trajectory of protein complexed with a ligand. I had gone through the
tutorial (http://www.amber.utah.edu/AMBER-workshop/London-2015/pca/) and
prepared this cpptraj script. Could you please let me know, if i am doing
this right?
Each of the trajectory has 5000 frames.
wat stands for protein in water
dov stands for protein complex with ligand
parm wat.prmtop [wat]
parm dov.prmtop [dov]
trajin wat.nc parm [wat]
trajin dov.nc parm [dov]
rms First :1-549.CA=
average crdset wat-dov-average
createcrd wat-dov-trajectories
crdaction wat-dov-trajectories rms ref wat-dov-average :1-549.CA=
crdaction wat-dov-trajectories matrix covar name wat-dov-covar :1-549.CA=
runanalysis diagmatrix wat-dov-covar out wat-dov-evecs-proj.dat vecs 3 name
myEvecs nmwiz nmwizvecs 3 nmwizfile pro_proj.nmd nmwizmask :1-549.CA=
crdaction wat-dov-trajectories projection wat modes myEvecs beg 1 end 3
:1-549.CA= crdframes 5002,last
hist wat:1 bins 100 out wat-dov-hist.agr norm name wat-1
hist wat:2 bins 100 out wat-dov-hist.agr norm name wat-2
hist wat:3 bins 100 out wat-dov-hist.agr norm name wat-3
clear all
readdata wat-dov-evecs-proj.dat name Evecs
parm wat.prmtop
parmstrip !(:1-549.CA=)
parmwrite out wat-dov-modes-proj.prmtop
runanalysis modes name Evecs trajout wat-dov-mode1-proj.nc pcmin -100 pcmax
100 tmode 1 trajoutmask :1-549.CA= trajoutfmt netcdf
Thank you in advance!

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Received on Thu Jul 18 2019 - 04:00:03 PDT
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