Hi,
On Sun, Feb 17, 2013 at 9:35 PM, Date, Mihir <Mihir.Date.stjude.org> wrote:
> 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
First I recommend that if you haven't already, you RMS-fit each frame
to an appropriate reference structure (average etc) prior to
calculating your matrix. Also, you don't need to explicitly specify
'&' in a residue/atom mask, i.e. :28.CA should work fine.
> This produces output for correlation function (corr.dat) but it has no data in it. Heres how the output looks like
Check your output and make sure that your masks are valid (you should
see something like "Mask [:28&.CA] represents 1 atoms". Also, note
that the code is set to ignore zero or negative eigenvalues by
skipping frequencies less than 0.5; check your eigenvalues in
evecs.dat.
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Mon Feb 18 2013 - 08:30:03 PST
