Is anything recent to account for (and eliminate) clashes - if any - resulting from solvating a system of protein partly immersed into a canonical DPPC bilayer? That is, the solvation water faces three different environments: the extracellular portion of the protein, the two water layers of DPPC, and the DPPC molecules themselves.
I was comfortable to this regard (in all-atoms) with Chimera followed by Amber minimization. I have to re-educate myself with gromacs-martini. With cg Chimera has so many limitations. I assume (for cg) that the box should first be defined with editconf and then solvation (-cs water.gro) carried out with genbox. thanks francesco On Tue, Dec 1, 2009 at 6:37 PM, XAvier Periole <[email protected]> wrote: > > On Dec 1, 2009, at 6:33 PM, XAvier Periole wrote: > >> >> you do not need itp file. in the top you'd find the parameters for >> the water. > > I mean in the top file you'll find the reference to the martini??.itp file > where the water is defined. >> >> On Dec 1, 2009, at 6:26 PM, Francesco Pietra wrote: >> >>> I forgot to ask, in additio to below, where to find the .itp file for >>> cg water. All that I have is water.gro water.mdp water.top from the >>> martini web site. >>> >>> >>> ---------- Forwarded message ---------- >>> From: Francesco Pietra <[email protected]> >>> Date: Tue, Dec 1, 2009 at 6:15 PM >>> Subject: Re: [gmx-users] Last step before CG em.mdp >>> To: [email protected], Discussion list for GROMACS users >>> <[email protected]> >>> >>> >>> On Mon, Nov 30, 2009 at 5:51 PM, Justin A. Lemkul <[email protected]> >>> wrote: >>>> >>>> >>>> Francesco Pietra wrote: >>> >>>>> cpp = /usr/bin/cpp >>>>> define = -DFLEX_SPC >>>> >>>> You're using SPC water in a coarse grain model? This doesn't make sense >>>> to >>>> me - an atomistic solvent with CG protein? >>> >>> In order to use this em.mdp, how to "define" cg water? Otherwise, is >>> it necessary at all to define the water used once there is a top file? >> >> no need to define. >>> >>> >>>> >>>> It's been many weeks now that you've posted some issues with your CG >>>> system, >>>> and I'm sorry but I can't recall - have you run through my membrane >>>> protein >>>> tutorial? It should be easily quite extended to a CG system. All of >>>> the >>>> fundamentals are the same as far as positioning the system, etc. go: >>>> >>>> >>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html >>> >>> My task is more complex than that, where you immerse the whole peptide >>> into the membrane. >>> >>> Actually, this is not my only interest, and I shift there when I find >>> some spare time. Also, I succeeded by using martini as implemented >>> into namd-vmd, but I would like to compare with gromacs. >> >> good idea. >>> >>> thanks >>> francesco >>> -- >>> gmx-users mailing list [email protected] >>> 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 [email protected]. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> -- >> gmx-users mailing list [email protected] >> 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 thewww interface >> or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- > gmx-users mailing list [email protected] > 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 thewww interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
