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.
