Aditi Borkar wrote:
Dear Rui,
Thanx for the explanation. I did not know that VMD only calculates the
secondary structure fort he first frame only. Is there an option to
calculate the secondary structure (say in New cartoon representation)
of all the frames in the trajectory?
You can use the Tcl interface to do it - the ssrecalc() function is designed for
that. Check out the VMD user's guide and their mailing list forum for how to
use it.
Even more quantitative, though, is to use do_dssp to get a plot of secondary
structure evolution.
-Justin
On Thu, Sep 24, 2009 at 5:39 PM, J. Rui Rodrigues
<joaquim.rodrig...@estg.ipleiria.pt> wrote:
Dear Aditi,
What do you mean with "evolution of the protein structure"? Are you referring to
*secondary structure*? By default, VMD only calculates it for the first
trajectory frame.
--Rui
On Thu, 24 Sep 2009 10:51:04 +0530, Aditi Borkar wrote
Dear All,
When I am loading the GROMACS trajectory in VMD, I cannot the
evolution of the protein structure with time.
When I am creating pdb files from the trajectory at different time
steps using the dump option, I do see changes in the protein structure
with time. My final structure after the MD simulation is also a lot
different that my start. However, when loading the trajectory, I do
not see a gradual/drastic transition from the starting to the final
conformation in VMD.
Please suggest where am I going wrong.
Thank you
--
Aditi Borkar,
Tata Institute of Fundamental Research,
Mumbai.
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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