On 9/19/14 5:15 PM, gromacs query wrote:
Hi Justin Hope it makes sense now :) Here is the link (small piece of some pdb without hydrogens) http://s000.tinyupload.com/?file_id=09348261523279878452 <http://s000.tinyupload.com/index.php?file_id=09348261523279878452> I used this command: (note residue 2 is missing so using 'r 2' will not work ) make_ndx -f test_noH.pdb -o ndx_noH.ndx selected as: r 3 It gives correct number of atoms info but gives atom numbers as line numbers (9 to 16) and 'real' atom numbers are: 34,36,38,41 ... so on It seems it reads residue column correctly from pdb, e.g. if you use r 2 then it complains that residue is missing but I think atom numbers are not read from 'atom number column' itself but as line numbers
make_ndx is assuming the coordinate file is numbered starting at 1, which is true for most coordinate files. If you renumber the file, then the make_ndx output matches the atom numbers in the coordinate file.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.
