[gmx-users] g_rms: Too many iterations in routine JACOBI

[Tsjerk Wassenaar]

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 <minnale_gnos at rediffmail.com> 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    gmx-users at gromacs.org
>  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 gmx-users-request at gromacs.org.
>  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