Thank you very much!
On Tue, Dec 17, 2013 at 10:25 AM, Justin Lemkul <jalem...@vt.edu> wrote: > On Tue, Dec 17, 2013 at 10:09 AM, Sidath Wijesinghe > <swij...@g.clemson.edu>wrote: > > > Justin, > > > > so that means delete these lines " > > ATOM 7882 SOD UNK 1 42.69 -261.86 64.056 1.00 0.00 > > UNK > > ATOM 7883 SOD UNK 1 39.09 -260.89 62.8968 1.00 0.00 > UNK > > ATOM 7884 SOD UNK 1 40.1388 -263.52 64.6776 1.00 0.00 > UNK > > ATOM 7885 SOD UNK 1 18.3684 -236.89 77.4756 1.00 0.00 > UNK > > ATOM 7886 SOD UNK 1 14.5668 -246.09 79.7592 1.00 0.00 > UNK > > ATOM 7887 SOD UNK 1 15.7704 -239.23 76.65 1.00 0.00 > UNK > > ATOM 7888 SOD UNK 1 14.7888 -242.75 78.6228 1.00 0.00 > UNK > > > > i have total of 48 sodium atoms... > > correspond to all the sodium atoms in test.pdb file and let it run with > > g_X2top? > > > > i am not clear about what u meant here... > > > > "Then modify > > the [molecules] directive to reflect the sodium ions and proceed with the > > intact coordinate file" > > > > > I'm suggesting you simplify what you are doing to try to give g_x2top a > break. It is not very adept at doing what you are trying to make it do. > You have sodium ions. They're not bonded to anything. They don't need to > be considered as one "molecule" along with the rest of the system. > Therefore, you don't need g_x2top to do anything with them. In a "normal" > Gromacs workflow, one takes a solute, gets a topology, adds some solvent > (using the #include mechanism for solvent, not generating a whole new > topology), then maybe adds some ions or other small molecules (again > #including a pre-existing topology) and the system is built. Now > reverse-engineer that. If you have some small species like ions, why > reinvent the wheel? You already have their topology in ions.itp, so you > just #include that in your final system topology and write the entry in > [molecules] yourself. > > If that's still confusing, please spend some time with tutorials (my own > lysozyme tutorial walks you through topology organization and how Gromacs > normally functions) and the manual, specifically Chapter 5. Then, once > you're comfortable with the file hierarchy and such, dive into g_x2top with > something simple, like one of your molecules, and make sure you know > exactly what's going on. Then add more layers of complexity until you get > the result you need or the program breaks completely ;) > > -Justin > > -- > > ========================================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > > ========================================== > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Sidath Wijesinghe Graduate Teaching Assistant Dept Of Chemistry Clemson University -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.