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?
Best regards Rasoul On Fri, Dec 18, 2009 at 10:04 PM, Justin A. Lemkul <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 | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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