Hi,
On Tue, Jan 20, 2015 at 6:40 AM, Suchetana Gupta bt13d072
<bt13d072.smail.iitm.ac.in> wrote:
> trajin last_20_stripped_imaged.cdf
> rms first mass :1-120
> matrix correl :1-120.CA out last_20_wt_correl.txt byres
>
> However, the output matrix file is not in a 120 X 120 format. Instead, I
> see data in a random fashion. So much so, that I am unable to understand
> which value corresponds to which residue. Is there any method to get the
> output in a 120X120 matrix?
It's not clear what you mean by "random fashion". Have you run the
tests for your Amber installation? You should absolutely get a file
containing 120 rows and 120 columns. Try it on a smaller number of
residues first to become familiar with the output. For example, a 4
residue selection (:1-4) will give output containing 4 rows and 4
columns like so:
1.00 0.38 0.23 0.02
0.38 1.00 0.46 -0.40
0.23 0.46 1.00 0.24
0.02 -0.40 0.24 1.00
The first row and column is residue 1 to 1, the first row and second
column is residue 1 to 2, etc. Hope this helps,
-Dan
PS - Also, consider upgrading to AmberTools 14 (which is free), as it
contains more functionality and bug fixes. Also consider using cpptraj
instead (ptraj is no longer being actively developed).
>
> Thanks in advance for your help
> Suchetana Gupta
> IIT Madras
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> AMBER.ambermd.org
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Jan 20 2015 - 10:30:03 PST
