rasoul nasiri wrote:
Hi,
Thank you for your quick reply.
Is there another CGFF for this purpose that Gromacs can read it? What is
your opinion about CG GO model?
There are several CG models out there, but I don't know much about them. The
nice thing about Gromacs is that it can use any force field you can find.
As for Go-models, you've already been given advice on that topic:
http://lists.gromacs.org/pipermail/gmx-users/2009-December/047496.html
-Justin
Kind regards
Rasoul
On Mon, Dec 21, 2009 at 8:23 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
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>
<mailto: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>
<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>
<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> <http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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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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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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