<!doctype html public "-//w3c//dtd html 4.0 transitional//en">
<html>
Hi all,
<br>i´m trying to do a covariance analysis on a combined trajectory.
When I join the two individual trajectories I only use the backbone.
<br>When I try to do the covariance analysis, using only the backbone for
the fit and for the covar analysis (i.e. the same atoms than in the trajectoy),
<br>I get the next error listed below.
<p>WARNING: masses will be determined based on residue and atom names,
<br> this can deviate from
the real mass of the atom type
<br>Opening library file /usr/local/gromacs/share/top/atommass.dat
<br>Opening library file /usr/local/gromacs/share/top/aminoacids.dat
<p>Choose a group for the least squares fit
<br>Group 0 ( Backbone) has
1002 elements
<br>There is one group in the index
<p>Choose a group for the covariance analysis
<br>Group 0 ( Backbone) has
1002 elements
<br>There is one group in the index
<p>Note: the fit and analysis group are identical,
<br> while the fit is mass weighted and the
analysis is not.
<br> Making the fit non mass weighted.
<br>
<p>Warning: can not make broken molecules whole without a run input file,
<br> don't worry, mdrun
doesn't write broken molecules
<p>Constructing covariance matrix (3006x3006)...
<br>Reading frame 0 time
0.000 Fatal error: Numerical Recipes: Too many iterations in
routine JACOBI
<p>Any help would be very appreciated!
<br>Thanks in advance,
<br>with best wishes,
<br>Ruben
<br>
<br>
<br>
<pre>--
___________________________________________
Rubén Martínez-Buey. PhD student
Protein Function and Structure Dept. Lab. 352
Centro de Investigaciones Biológicas (CIB-CSIC)
C/ Velázquez, 144, 28006 MADRID (SPAIN)
Tlf: +34-91-561 18 00 ext. 4380
Fax: +34-91-562 75 18</pre>
</html>