jayant james wrote:
Hi!
I have appended the NMR structure to a part of the protein that was not
resolved to the protein and now I want to perform simulated annealing of
the 40 amino acids (NMR structure had 33 amino acids and to link I
needed another 7 aa) that have been thrown into the crystal structure. I
am new to this simulated annealing procedure. So please help me out as
how to write out a typical pr.mdp file. I am thinking of increasing the
temp of the appended piece protein piece to about 10000K (while the rest
of the protein, solvent, Na+ and Cl- are at 300K) and slowly bring the
temperature down to 300K, say, in about 100 ps and then continue to
perform MD simulations.
Running a protein segment at 10000 K with solvent at 300 K will probably lead to
some wild behavior of that protein segment, clashes with the solvent, and
possibly an explosion of your system. Just thinking ahead...
1) So would it be the wise time to apply distance constraints from the
protein at 300K to the appended peptide while performing simulated
annealing?
If you have actual NMR data, perhaps. But attempting to simulate at 10000 K
while simultaneously applying distance restraints might be a difficult task
(consider a lower temperature).
2) If so what would be a good temperature to set it to kick in? I am
really confused as to how I am going to specify these 40 residues to be
the group that needs to be heated up.
Warm it up from some low temperature. There is an example at:
http://www.gromacs.org/documentation/reference_4.0/online/mdp_opt.html#sa
If you want a separate temperature coupling group, make a special index group
for it. No idea if that will actually work, but that's how you treat components
of your system differently, in general.
3) Usually I have tc-grps specified in pr.mdp as Protein and
Non-Protein. So how would I go about setting up the temperature groups
during the simulated annealing protocol?
With the special index group. See #2.
-Justin
Thanks
JJ
On Thu, Feb 26, 2009 at 4:47 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
jayant james wrote:
Hi!
I have a question with regard to a system that I am attempting
to model.
The N-terminal of chain of the protein was not resolved
crystallographically but was later solved by NMR.
Now my plan is to append the NMR structure on to chain A of the
protein and perform simulated annealing only for the appended
NMR fragment. To help it find it biologically relevent
orientation in the system I could also apply distance restraints
that I have.
Is this possible in Gromacs?
All except that actual construction part (modeling the two segments
together), yes.
-Justin
thanks
JJ
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
Jayasundar Jayant James
www.chick.com/reading/tracts/0096/0096_01.asp
<http://www.chick.com/reading/tracts/0096/0096_01.asp>)
--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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