Dear all, so after I opened angle.ndx file in a text editor, the file appears to be blank. How can I properly make a index file since the command I issued seems to produce a blank index file? Is there something wrong with my input regarding npt.tpr?
Thanks for your input, Xu Huang On Oct 31, 2013, at 1:38 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/31/13 1:36 PM, Xu Dong Huang wrote: >> Dear all. >> >> Since I am interested in finding the average angle, dihedrals in my system, >> I attempted to use g_angle, but then I realized I need to make index file >> using mk_angndx, >> >> I issued the following: >> mk_angndx -s npt.tpr -n angle.ndx >> >> and then i used g_angle -f not.xtc -n angle.ndx -ov angle.xvg -noperiodic >> -type angle >> >> and then I get the following error: >> Fatal error: >> Error: no groups in indexfile >> >> How can my index file not have the groups in there? How can I go about >> fixing this >> > > Inspect it with a text editor and/or gmxcheck. > > -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 > > ================================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
