Hi,<br>Thank you for your quick reply.<br><br>Is there another CGFF for this purpose that Gromacs can read it? What is your opinion about CG GO model? <br><br>Kind regards<br>Rasoul<br> <br><br><div class="gmail_quote">On Mon, Dec 21, 2009 at 8:23 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im"><br>
<br>
rasoul nasiri wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Justin,<br>
Thank you for your message.<br>
<br>
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.<br>
Could I perform CGMD simulation with MArtini force field for finding the denaturation mechanism of the protein properly?<br>
<br>
</blockquote>
<br></div>
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?<br>
<br>
Net result: this particular CG model is probably not suitable for such a simulation.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Best regards<br>
Rasoul<div class="im"><br>
<br>
On Fri, Dec 18, 2009 at 10:04 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
rasoul nasiri wrote:<br>
<br>
Dear Cesar,<br>
Thank you for your reply,<br>
<br>
There are two different kind of water gro in this site (one of<br>
them is water.gro in :<br>
<a href="http://md.chem.rug.nl/%7Emarrink/MARTINI/Coordinates.html" target="_blank">http://md.chem.rug.nl/~marrink/MARTINI/Coordinates.html</a><br></div>
<<a href="http://md.chem.rug.nl/%7Emarrink/MARTINI/Coordinates.html" target="_blank">http://md.chem.rug.nl/%7Emarrink/MARTINI/Coordinates.html</a>> and<div class="im"><br>
another is water-1bar-303k.gro in :<br>
<a href="http://md.chem.rug.nl/%7Emarrink/MARTINI/Tutorial.html" target="_blank">http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.html</a><br></div>
<<a href="http://md.chem.rug.nl/%7Emarrink/MARTINI/Tutorial.html" target="_blank">http://md.chem.rug.nl/%7Emarrink/MARTINI/Tutorial.html</a>> . Is<div><div></div><div class="h5"><br>
there difference between them?<br>
<br>
<br>
Maybe, but if you do sufficient equilibration, it probably won't matter.<br>
<br>
<br>
Can I build water.gro with coarse graining beads (P4) from<br>
spc216.gro with using atom2cg.awk script?<br>
<br>
<br>
No. This has been stated before - the awk script is explicitly for<br>
protein. And besides, each "W" CG particle corresponds to about four<br>
water molecules, so there is no trivial way to decide how to build<br>
the CG water system from spc216.gro.<br>
<br>
<br>
Another question; How can I change secondary structure<br>
information during CGMD simulation, If I want to perform CGMD<br>
simulation for finding of the folding/unfolding mechanism in<br>
proteins completely? Because Martini CGFF consider fix it.<br>
<br>
<br>
You specify the secondary structure when building the initial<br>
topology. As you've been advised already, this "fixed"<br>
representation of secondary structure is going to be a major<br>
limitation of using the MARTINI force field for your simulations.<br>
How do you know that whatever alternate secondary structure you've<br>
applied is valid? If you have some experimental evidence to suggest<br>
that certain peptide regions convert between one form and another,<br>
that's fine, but how do you know that the pathway taken is not an<br>
artifact of your choice to abruptly impose a change in the topology?<br>
<br>
<br>
-Justin<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
-- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><div class="im"><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br>
posting!<br>
Please don't post (un)subscribe requests to the list. Use the www<br>
interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.<div class="im"><br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
<br>
</div></blockquote><div><div></div><div class="h5">
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</div></div></blockquote></div><br>