Hi,
I wish to conduct PCA on a helical segment of a full protein. My script is as follows:
cat << EOF >> trajin1
trajin 10to50ns-dry.mdcrd 10001 40000
rms first :353-367.CA
matrix covar :353-367.CA name mcovar
analyze matrix mcovar out evec.pev vecs 10
go
EOF
ptraj complex_dry2.top < trajin1
#
cat << EOF >> trajin2
trajin 10to50ns-dry.mdcrd 10001 40000
rms first :353-367.CA
projection modes evec.pev out proj.ppj beg 1 end 10 :353-367.CA
go
EOF
ptraj complex_dry2.top < trajin2
However, when I visualised it using VMD, the eigenmotions look distorted. Therefore, I wish to confirm if the script above is logical. If so, the topol.pdb that I use should be the full protein instead of the segment which I did PCA on, right?
Thanks.
Regards
Yip Yew Mun
Graduate, PhD
Chemistry and Biological Chemistry
School of Physical and Mathematical Sciences
Nanyang Technological University
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Received on Sat Apr 19 2014 - 22:00:08 PDT
