Dear experts,
I would like to calculate rotational diffusion of exocyclic hydroxyl group
in sugar (glucose) molecule in a hydrated lipid bilayer system.
Well, I generated a single PDB file of the system to be used as *reference*
and executed command as below:
*system="bcmLyo25perR"trajPath="/home/users/vijay/slot3/paper3-lyo-system-TRAJ-Only/onlyTraj-$system"top="$trajPath/$system.prmtop"TRAJ="$trajPath/md-all-$system.nc
<
http://system.nc>"cpptraj $top << EOFreference
$trajPath/md-all-bcmLyo25perR.nc.pdb.1 [avg]trajin $TRAJ 15001 16000unwrap
*rotdif nvecs 1000 ref [avg] :1.C25,C26,O26,H26 \ncorr 400 ti 0.0 tf 1 dt
0.001 deffout deffs.dat \itmax 100 tol 0.000001 d0 0.03 order 2 \outfile
rotdif.out*
*EOF*
I got the above command from Ambertool14 manual (page 545).
The calculation went without error. I got two files and I don't understand
the contents of the files (also the format tough).
I used 1000 frames for analysis. I have attached those files for your view
as well.
Hope to get some explanation.
Thank you.
Vijay
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Received on Fri Feb 13 2015 - 03:30:03 PST
