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 On Fri, Sep 19, 2014 at 9:37 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/19/14 8:43 AM, gromacs query wrote: > >> Hi All >> >> I have some pdb file and I removed hydrogens. When I try to make ndx file >> using some residue option then rather printing atom numbers in that >> residue >> it prints line number where that residue starts and ends. >> >> make_ndx -f no_H.pdb -o test.ndx >> >> selecting as: >> >> r 300-330 >> >> Then in ndx file I get the line number where residue number 300 starts >> (not >> the atom number). I think hydrogens were missing so it just uses line >> number. >> > > This doesn't make any sense. make_ndx doesn't process line numbers. Can > you give an excerpt (or even better, upload the whole file somewhere) of > the index file to show what you mean? The coordinate file would be > helpful, too. > > -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. > -- 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.