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

minnale minnale_gnos at rediffmail.com
Thu May 8 09:18:58 CEST 2008


  
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.
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