On 4/12/18 2:12 PM, Andrew DeYoung wrote:
Hi, I am running Gromacs 4.5.5. In that rather old version, there is a binary called g_x2top -- I think it is now called something else -- to generate "a primitive topology from a coordinate file." When I use g_x2top with my (custom) force field, g_x2top generates a nicely formatted topology file (either .top or .itp). Here is a snippet from the nicely formatted topology (assuming you display the text in a fixed width font): [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 c4 c5 81 97 113 129 1 112 97 113 114 1 112 97 113 129 1 82 98 99 83 1 82 98 99 115 1 (Only atom indices and a function type are printed because I used the option -noparam in g_x2top.) But, what if I want to generate my own .top or .itp text file, using for example Fortran, Perl, or Python? Are .top and .itp fixed-spaced file formats? In other words, do I have to nicely align the columns as g_x2top does? Or can I just use any number of spaces to delimit the columns, like in the following example? [ dihedrals ] 81 97 113 129 1 112 97 113 114 1 112 97 113 129 1 82 98 99 83 1 82 98 99 115 1 I have tried this ugly formatting, and it seems to give the same results as the nice formatting. But can anyone confirm that .top and .itp are NOT fixed-spaced file formats (unlike .pdb and .gro for example)?
GROMACS topologies are free format. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- 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.