Hi JS RED, This usually indicates that you have a mismatch between your reference structure and your trajectory, which is logical as you extracted a specific set of coordinates from the trajectory, but used an original (complete) gro file.
Hope it helps, Tsjerk On Thu, May 8, 2008 at 9:18 AM, minnale <[EMAIL PROTECTED]> wrote: > > > > Hi all, > 1)I made make_ndx file for my protein because i want to plot rmsd for > specific residues in protein, so I have givenlike this 1 & r 50-80 > > 2)Then I have used trjcat -f 1ns.xtc 2ns.xtc 3ns.xtc -n r_50_80.ndx > -settime -o trjout , here I selected > Protein_&_r_50-80 > this command ran without error, > > 3)After, > g_rms -f trjout.xtc -pbc -s em_inti.gro -pbc -o rms_3ns > Select group for least squares fit - 3 c-alpha > Select group for RMSD calculation - 3 c-alpha > it showed following error > > Program g_rms, VERSION 3.3.1 > Source code file: nrjac.c, line: 129 > > Fatal error: > Error: Too many iterations in routine JACOBI > I have searched in gmx archives regarding this problem , I found that > mismatch between trjactory and reference structure file, but in my case both > are matched atoms > > Is there any mistake in either selecting options of making index file or I > have given wrong option while using g_rms > > Pls suggest me > Thanks in advance. > > > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
