rasoul nasiri wrote:
Dear Justin,
Thank you for your message.
I have found some experimental evidence to suggest that the secondary
structure information of protein how change during the reaction of the
unfolding. In the other hand, I have percentage of the secondary
structure information (%alpha-Helix, %beta-sheet and %Random coil) of
the protein at different time of reaction.
Could I perform CGMD simulation with MArtini force field for finding the
denaturation mechanism of the protein properly?
I would be extremely suspicious of any results you get. As you've been told
before, secondary structure is a fixed aspect of a MARTINI CG simulation.
Making changes is somewhat arbitrary and may lead to artifacts that you can't
anticipate. Besides, if you only know percentages of secondary structure (from
CD I assume?) then you don't really know the structures and sequences that are
changing, do you?
Net result: this particular CG model is probably not suitable for such a
simulation.
-Justin
Best regards
Rasoul
On Fri, Dec 18, 2009 at 10:04 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
rasoul nasiri wrote:
Dear Cesar,
Thank you for your reply,
There are two different kind of water gro in this site (one of
them is water.gro in :
http://md.chem.rug.nl/~marrink/MARTINI/Coordinates.html
<http://md.chem.rug.nl/%7Emarrink/MARTINI/Coordinates.html> and
another is water-1bar-303k.gro in :
http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.html
<http://md.chem.rug.nl/%7Emarrink/MARTINI/Tutorial.html> . Is
there difference between them?
Maybe, but if you do sufficient equilibration, it probably won't matter.
Can I build water.gro with coarse graining beads (P4) from
spc216.gro with using atom2cg.awk script?
No. This has been stated before - the awk script is explicitly for
protein. And besides, each "W" CG particle corresponds to about four
water molecules, so there is no trivial way to decide how to build
the CG water system from spc216.gro.
Another question; How can I change secondary structure
information during CGMD simulation, If I want to perform CGMD
simulation for finding of the folding/unfolding mechanism in
proteins completely? Because Martini CGFF consider fix it.
You specify the secondary structure when building the initial
topology. As you've been advised already, this "fixed"
representation of secondary structure is going to be a major
limitation of using the MARTINI force field for your simulations.
How do you know that whatever alternate secondary structure you've
applied is valid? If you have some experimental evidence to suggest
that certain peptide regions convert between one form and another,
that's fine, but how do you know that the pathway taken is not an
artifact of your choice to abruptly impose a change in the topology?
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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