Thnaks for your help Tsjerk.
One more thing I didnt understand is, if use all same commands except choosing
options in make_ndx file like " 1 | r 50-80 " generated rmsd.xvg without
issuing error, but if i use below mentioned commnands showing error, which way
is correct?
Thanks for your appreciation
>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.
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