Hi,
On Fri, Feb 13, 2015 at 4:00 AM, Vijay Achari <glycoamber.gmail.com> wrote:
> I would like to calculate rotational diffusion of exocyclic hydroxyl group
> in sugar (glucose) molecule in a hydrated lipid bilayer system.
The 'rotdif' command is really intended for calculating the rotational
diffusion tensor for a whole molecule, not parts of one. I suggest
reading the Wong & Case paper that goes into detail on the procedure
that is used by 'rotdif': http://www.ncbi.nlm.nih.gov/pubmed/18052365
-Dan
>
> Well, I generated a single PDB file of the system to be used as *reference*
>
> and executed command as below:
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> *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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>
--
-------------------------
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 Sun Feb 15 2015 - 09:00:03 PST
