if i refine the chaps.itp with opls charges, will it be active?
If not, what can i do then? should i use cholesterol in place of chaps? if yes, where to do download from ? --- On Fri, 13/6/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > From: Justin A. Lemkul <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] bicelle gromacs MD simulation CG model? > To: [EMAIL PROTECTED] > Cc: "Gromacs Users' List" <gmx-users@gromacs.org> > Date: Friday, 13 June, 2008, 4:50 PM > ANINDITA GAYEN wrote: > > I have build the itp file from PRODG2 DUNDEE server. > and then replaced the stom types from OPLS. Can you comment > about the itp file, i can serve that to u. > > > > > > Please make sure you are replying to the gmx-users > listserv; that way > this thread will be archived for others to benefit from in > the future. > > I don't think your approach is very sound. The PRODRG > server generates > GROMOS-compatible topologies, so supplying OPLS atom types > with GROMOS > bond, angle, etc. parameters probably will not lead to a > very > self-consistent topology. > > As a general note, be aware that the charges and charge > groups assigned > by PRODRG are often unsatisfactory, and require refinement. > > -Justin > > > --- On Fri, 13/6/08, Justin A. Lemkul > <[EMAIL PROTECTED]> wrote: > > > > > >> From: Justin A. Lemkul <[EMAIL PROTECTED]> > >> Subject: Re: [gmx-users] bicelle gromacs MD > simulation CG model? > >> To: [EMAIL PROTECTED] > >> Cc: "Gromacs Users' List" > <gmx-users@gromacs.org> > >> Date: Friday, 13 June, 2008, 4:25 PM > >> ANINDITA GAYEN wrote: > >> > >>> You can find my paper on Langmuir vol 24, > Issue 10, > >>> > >> pages 5422-5432 2008, I have made two bicelle > samples > >> experimentally, and now i want to model those two > bicelles > >> theorically to connect the theory with the NMR > experimental > >> data. I have euilibrated a dmpc bilayer in > OPLS-BERGER force > >> field already, but confused about the > incorporation of chaps > >> since it is not a bilayer component. I have 128 > lipid square > >> bilayer. Is it possible to model such a bilayer > that will > >> have chaps at the edge from this force field or > may i use > >> the coarse grain model to build it? can you > suggest > >> anything? > >> > >>> > >>> > >> Conceivably, you could do either, as long as the > parameters > >> you derive > >> are with are consistent with the original force > field. It > >> won't be > >> easy; the structure of CHAPS has some odd > functional groups > >> to deal > >> with, so I don't know that the existing Berger > lipid > >> parameters will be > >> applicable, but that doesn't mean they > couldn't be > >> extended to include > >> your molecule. As for a CG model, there are also > some > >> challenges there, > >> as well. There is a CG topology for cholesterol > online, > >> which could > >> serve as a starting framework for CHAPS, but > applying the > >> appropriate > >> particles to the rest of the molecule (quaternary > amine, > >> sulfate) would > >> require thorough evaluation of the atom types > available in > >> MARTINI. > >> > >> -Justin > >> > >> > >>> --- On Fri, 13/6/08, Justin A. Lemkul > >>> > >> <[EMAIL PROTECTED]> wrote: > >> > >>> > >>> > >>>> From: Justin A. Lemkul > <[EMAIL PROTECTED]> > >>>> Subject: Re: [gmx-users] bicelle gromacs > MD > >>>> > >> simulation CG model? > >> > >>>> To: [EMAIL PROTECTED], > "Discussion > >>>> > >> list for GROMACS users" > <gmx-users@gromacs.org> > >> > >>>> Date: Friday, 13 June, 2008, 3:54 PM > >>>> Can you be more specific as to what you > need help > >>>> > >> on? > >> > >>>> I'm familiar with > >>>> a couple of these papers, and the methods > sections > >>>> > >> are > >> > >>>> quite good. > >>>> Files are freely available on S.J. > Marrink's > >>>> > >> site, as > >> > >>>> well as a list of > >>>> pertinent publications detailing their > >>>> > >> methodology. > >> > >>>> -Justin > >>>> > >>>> ANINDITA GAYEN wrote: > >>>> > >>>> > >>>>> --- On Fri, 13/6/08, ANINDITA GAYEN > >>>>> > >>>>> > >>>> <[EMAIL PROTECTED]> wrote: > >>>> > >>>> > >>>>> > >>>>> > >>>>> > >>>>>> From: ANINDITA GAYEN > >>>>>> > >>>>>> > >>>> <[EMAIL PROTECTED]> > >>>> > >>>> > >>>>>> Subject: > >>>>>> To: gmx-users@gromacs.org > >>>>>> Date: Friday, 13 June, 2008, 9:56 > AM > >>>>>> Hi, > >>>>>> > >>>>>> I several papers of Marrink, > Siewert J.; > >>>>>> > >> Mark, > >> > >>>>>> > >>>>>> > >>>> Alan E, > >>>> > >>>> > >>>>>> and in a paper of Yong Jiang, > bicelles are > >>>>>> > >> modeled > >> > >>>>>> > >>>>>> > >>>> with CG > >>>> > >>>> > >>>>>> model. > >>>>>> > >>>>>> JCP 126, 045105 (2007) Jiang Y. > >>>>>> Biophys. j. 87 182-192 Jiang Y. > >>>>>> Effect of Undulations on Surface > Tension > >>>>>> > >> in > >> > >>>>>> > >>>>>> > >>>> Simulated > >>>> > >>>> > >>>>>> Bilayers > >>>>>> > >>>>>> Marrink, S. J.; Mark, A. E. J. > Phys. Chem. > >>>>>> > >> B.; > >> > >>>>>> > >>>>>> > >>>> (Article); > >>>> > >>>> > >>>>>> 2001; 105(26); 6122-6127. DOI: > >>>>>> > >> 10.1021/jp0103474. > >> > >>>>>> Molecular Dynamics Simulations of > Mixed > >>>>>> > >> Micelles > >> > >>>>>> > >>>>>> > >>>> Modeling > >>>> > >>>> > >>>>>> Human Bile > >>>>>> > >>>>>> Marrink, S. J.; Mark, A. E. > >>>>>> Biochemistry; (Article); 2002; > 41(17); > >>>>>> > >> 5375-5382. > >> > >>>>>> Molecular Dynamics Simulation of > the > >>>>>> > >> Kinetics of > >> > >>>>>> Spontaneous Micelle Formation > >>>>>> Marrink, S. J.; Tieleman, D. P.; > Mark, A. > >>>>>> > >> E. > >> > >>>>>> J. Phys. Chem. B.; (Article); > 2000; > >>>>>> > >> 104(51); > >> > >>>>>> > >>>>>> > >>>> 12165-12173. > >>>> > >>>> > >>>>>> Can someone help me? > >>>>>> > >>>>>> > >>>>>> Message: 7 > >>>>>> Date: Fri, 13 Jun 2008 02:21:48 > +1000 > >>>>>> From: Mark Abraham > >>>>>> > >> <[EMAIL PROTECTED]> > >> > >>>>>> Subject: Re: [gmx-users] bicelle > gromacs > >>>>>> > >> MD > >> > >>>>>> > >>>>>> > >>>> simulation CG > >>>> > >>>> > >>>>>> model? > >>>>>> To: Discussion list for GROMACS > users > >>>>>> <gmx-users@gromacs.org> > >>>>>> Message-ID: > >>>>>> > >> <[EMAIL PROTECTED]> > >> > >>>>>> Content-Type: text/plain; > charset=UTF-8; > >>>>>> > >>>>>> > >>>> format=flowed > >>>> > >>>> > >>>>>> ANINDITA GAYEN wrote: > >>>>>> > >>>>>> > >>>>>> > >>>>>>> hi all, > >>>>>>> > >>>>>>> can someone give me > information how to > >>>>>>> > >> model a > >> > >>>>>>> > >>>>>>> > >>>> bicelle > >>>> > >>>> > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>> using gromacs? I have dmpc:chaps > as the > >>>>>> > >> bicelle > >> > >>>>>> > >>>>>> > >>>> components, > >>>> > >>>> > >>>>>> and i came to know that coarse > grain model > >>>>>> > >> can > >> > >>>>>> > >>>>>> > >>>> help me. > >>>> > >>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>>> But, the picture is still not > clear. > >>>>>>> > >> Please > >> > >>>>>>> > >>>>>>> > >>>> help me to > >>>> > >>>> > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>> make the bicelle in gromacs. > >>>>>> > >>>>>> Have you searched the web and the > >>>>>> > >> literature to > >> > >>>>>> > >>>>>> > >>>> see if > >>>> > >>>> > >>>>>> anybody else has > >>>>>> done something like this? > >>>>>> > >>>>>> > >>>>>> > >>>>>> Bring your gang together. Do > your > >>>>>> > >> thing. > >> > >>>>>> > >>>>>> > >>>> Find your > >>>> > >>>> > >>>>>> favourite Yahoo! group at > >>>>>> http://in.promos.yahoo.com/groups/ > >>>>>> > >>>>>> > >>>>>> > >>>>> Explore your hobbies and > interests. Go > >>>>> > >> to > >> > >>>>> > >>>>> > >>>> http://in.promos.yahoo.com/groups/ > >>>> > >>>> > >> _______________________________________________ > >> > >>>>> gmx-users mailing list > >>>>> > >> gmx-users@gromacs.org > >> > >> http://www.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 > >>>> > >>>> > >>>>> > >>>>> > >>>>> > >>>> -- > >>>> ======================================== > >>>> > >>>> Justin A. Lemkul > >>>> Graduate Research Assistant > >>>> Department of Biochemistry > >>>> Virginia Tech > >>>> Blacksburg, VA > >>>> jalemkul[at]vt.edu | (540) 231-9080 > >>>> > >>>> > >> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > >> > >>>> ======================================== > >>>> > >>>> > >>> Unlimited freedom, unlimited storage. > Get it > >>> > >> now, on > >> > http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/ > >> > >>> > >>> > >> -- > >> ======================================== > >> > >> Justin A. Lemkul > >> Graduate Research Assistant > >> Department of Biochemistry > >> Virginia Tech > >> Blacksburg, VA > >> jalemkul[at]vt.edu | (540) 231-9080 > >> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > >> > >> ======================================== > >> > > > > > > Meet people who discuss and share your passions. > Go to http://in.promos.yahoo.com/groups/bestofyahoo/ > > > > > > > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== Did you know? You can CHAT without downloading messenger. Go to http://in.messenger.yahoo.com/webmessengerpromo.php/ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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