On 2/11/13 9:16 PM, ram bio wrote:
Hi Justin,
Thanks for the suggestion.
I executed the following command:
g_dist -f n101c2naclprod2-12nsvrpr.trr -s
n101c2naclpose2prod2nsvrpr.tpr -n index.ndx -dist 0.35 -o
N101Cbest2NACL606S336HG1.xvg
and the output was distance calculated for every 10 frames in nm as under:
t: 11870 336 SER 4166 HG1 0.239086 (nm)
t: 11880 336 SER 4166 HG1 0.248868 (nm)
t: 11890 336 SER 4166 HG1 0.231819 (nm)
t: 11900 336 SER 4166 HG1 0.218495 (nm)
t: 11910 336 SER 4166 HG1 0.233166 (nm)
t: 11920 336 SER 4166 HG1 0.283512 (nm)
t: 11930 336 SER 4166 HG1 0.239512 (nm)
t: 11940 336 SER 4166 HG1 0.216938 (nm)
t: 11950 336 SER 4166 HG1 0.220066 (nm)
t: 11960 336 SER 4166 HG1 0.227595 (nm)
t: 11970 336 SER 4166 HG1 0.247895 (nm)
t: 11980 336 SER 4166 HG1 0.259074 (nm)
t: 11990 336 SER 4166 HG1 0.228319 (nm)
t: 12000 336 SER 4166 HG1 0.264722 (nm)
So, my question is that now do maths and find percent frames that
were above the 3.5 Å and expresses it relation to unity for occupancy.
That is if i have 30 frames above 3.5Å out of 100, then the occupancy
would be 0.7.
Please advice if there is any other ways to do it..
Redirect the output into a file, count the number of lines in the file with wc
-l and you have the answer.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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