Amber users,
I want to calculate pair correlation function through PCA using analyze command. Following are my commands that I use for cpptraj,
trajin ../prod.mdcrd
matrix mwcovar name mwcvmat :1-275.CA,N,C,O out mwcvmat.dat
analyze matrix mwcvmat name evecs out evecs.dat vecs 30
analyze modes corr out corr.dat stack evecs beg 1 end 3 maskp :28&.CA :235&.CA
This produces output for correlation function (corr.dat) but it has no data in it. Heres how the output looks like
$ cat corr.dat
Analysis of modes: CORRELATION FUNCTIONS
Atom1 Atom2 Mode Freq 1-S^2 P2(cum)
445 3638
Are there any obvious mistakes in the commands that I am using ?
Can anybody point it out?
Thank you,
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Received on Sun Feb 17 2013 - 21:00:02 PST
