<P>
<BR>
Thnaks for your help Tsjerk.<BR>
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? <BR>
Thanks for your appreciation<BR>
<BR>
<BR>
>Hi JS RED,<BR>
<BR>
>This usually indicates that you have a mismatch between your reference<BR>
>structure and your trajectory, which is logical as you extracted a<BR>
>specific set of coordinates from the trajectory, but used an original<BR>
>(complete) gro file.<BR>
<BR>
>Hope it helps,<BR>
<BR>
Tsjerk<BR>
<BR>
On Thu, May 8, 2008 at 9:18 AM, minnale <minnale_gnos at rediffmail.com> wrote:<BR>
><BR>
><BR>
><BR>
> Hi all,<BR>
> 1)I made make_ndx file for my protein because i want to plot rmsd for<BR>
> specific residues in protein, so I have givenlike this 1 & r 50-80<BR>
><BR>
> 2)Then I have used trjcat -f 1ns.xtc 2ns.xtc 3ns.xtc -n r_50_80.ndx<BR>
> -settime -o trjout , here I selected<BR>
> Protein_&_r_50-80<BR>
> this command ran without error,<BR>
><BR>
> 3)After,<BR>
> g_rms -f trjout.xtc -pbc -s em_inti.gro -pbc -o rms_3ns<BR>
> Select group for least squares fit - 3 c-alpha<BR>
> Select group for RMSD calculation - 3 c-alpha<BR>
> it showed following error<BR>
><BR>
> Program g_rms, VERSION 3.3.1<BR>
> Source code file: nrjac.c, line: 129<BR>
><BR>
> Fatal error:<BR>
> Error: Too many iterations in routine JACOBI<BR>
> I have searched in gmx archives regarding this problem , I found that<BR>
> mismatch between trjactory and reference structure file, but in my case both<BR>
> are matched atoms<BR>
><BR>
> Is there any mistake in either selecting options of making index file or I<BR>
> have given wrong option while using g_rms<BR>
><BR>
> Pls suggest me<BR>
> Thanks in advance.
</P>
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