On Mon, Oct 27, 2008 at 10:21 AM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
> > > Peyman Yamin wrote: > >> On Monday 27 October 2008 15:07, Justin A. Lemkul wrote: >> >>> Peyman Yamin wrote: >>> >>>> On Monday 27 October 2008 14:03, Justin A. Lemkul wrote: >>>> >>>> Actually I'm doing a funny mistake telling I should replace an O with an >>>> Na! (probably because of high adrenaline level in my blood for the >>>> deadline is near!) I should just put one Na beside the O I have! I >>>> simply >>>> have a PO4 where one O has no H and thus is negative. an Na+ should >>>> accompany this O. >>>> >>> Well that makes more sense. I'm assuming you have a DPPG bilayer with >>> solvent? Or are you simulating a single DPPG in vacuo? If it's a bilayer >>> in solution, just use genion; you can even specify exactly how many Na+ >>> you >>> want using -np. >>> >>> If the topology organization is confusing you, refer to Chapter 5 of the >>> manual. If you make a .top for DPPG, you can specify: >>> >>> [ molecules ] >>> DPPG x >>> NA+ 1 (or whatever) >>> >>> after including the appropriate force field call and ions.itp; the >>> parameters for all atom types are taken from these files. >>> >> >> Well this looks great! I simulate one single DPPG in solvent. and you >> know, this Na+ is not in solvent but a part of DPPG. So you mean I just make >> a DPPG with an O which has no H so is minus and then use genion to add Na? >> will it place the Na aroung O hopefully? I think if I put no H arounf O the >> prodrg will force me to have it! so I should delete it and replace it with >> Na? or I should never use the word "replace" at all??? >> >> > Well, the Na+ may be associated with DPPG electrostatically, but they are > still distinct chemical entities. You can have a DPPG that has a net -1 > charge; certainly all chemical species are not net neutral! Indeed, genion > will place Na+ in whatever solvent you choose, but may not necessarily be > bound to DPPG. Some simulation may show the association, however. > Yes, keep the DPPG. The charge distribution around anionic lipid has been studied. http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=PRLTAO000101000003038103000001&idtype=cvips&gifs=yes > > And no, don't replace any part of your DPPG. Because then you don't really > have DPPG any more do you? > > -Justin > > > Thanks again ;) >> Peyman >> >> -Justin >>> >>> Peyman Yamin wrote: >>>>> >>>>>> Dear GMX users, >>>>>> >>>>>> I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the >>>>>> structure with the Na replaced with O. I get a .top with this from >>>>>> prodrg and try to add the Na manually at the right place by removing >>>>>> the corresponding O. I use GROMOS 96.1 forcefield. GMX version 3.3.1.I >>>>>> have a problem: >>>>>> >>>>> Are you trying to replace the O in DPPG with Na+? Or are you simply >>>>> trying to add ions to the surrounding solvent (water)? If you just >>>>> need >>>>> ions in the solvent, use genion; you don't have to do it manually. >>>>> >>>>> * In .top file, as far as I can understand, I should just replace OA >>>>>> with NA+ and set the mass and charge. >>>>>> DPPG has a centre: [ O-P(O)=O ] - >>>>>> The Na+ should be around this with +1 charge. >>>>>> should I put charge +1 ? >>>>>> >>>>> Again, I'm not clear on what you're trying to accomplish. If you >>>>> replace one of these oxygen atoms, you will likely not have an integer >>>>> charge within the DPPG molecule itself. >>>>> >>>>> * which parameters should I place in the top as the Na+ is not >>>>>> bonding. >>>>>> I need LJ and Coulomb params. I have C6 and C12 them from >>>>>> ffG43a1nb.itp. (NA+ OA) but I'm not sure where should I put it in the >>>>>> top file. What should I insert manually in top file at all? >>>>>> >>>>> Simply #include "ffG43a1.itp" at the top of your .top file; it will >>>>> include nonbonded and bonded parameters for all the atoms in the >>>>> system. >>>>> >>>>> -Justin >>>>> >>>>> Thanks in advance for the time, >>>>>> I've been away for some time from GMX and might sound >>>>>> >>>>>> Cheers, >>>>>> Peyman >>>>>> >>>>> >> > -- > ======================================== > > 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 > > ======================================== > _______________________________________________ > gmx-users mailing list [email protected] > 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 > -- Best wishes, Myunggi Yi ================================== KLB 419 Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306 Office: (850) 645-1334 http://www.scs.fsu.edu/~myunggi [EMAIL PROTECTED]
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