<P>
<BR>
Hi all, <BR>
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<BR>
<BR>
2)Then I have used trjcat -f 1ns.xtc 2ns.xtc 3ns.xtc -n r_50_80.ndx -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 mismatch between trjactory and reference structure file, but in my case both are matched atoms<BR>
<BR>
Is there any mistake in either selecting options of making index file or I have given wrong option while using g_rms<BR>
<BR>
Pls suggest me<BR>
Thanks in advance.
</P>
<br><br>
<Table border=0 Width=644 Height=57 cellspacing=0 cellpadding=0 style='font-family:Verdana;font-size:11px;line-height:15px;'><TR><td><img src ='http://imadworks.rediff.com/cgi-bin/AdWorks/adimage.cgi/2087310_2079844/creative_2087453.jpg' alt='JS RED' border=0></td></TR></Table>