[gmx-users] problem with structure factor in g_rdf

jagannath mondal jmondal2004 at yahoo.co.in
Sun Feb 17 10:40:23 CET 2008

   I  was trying to use g_rdf analysis tool to
calculate the structure factor of 
 a polymer I am simulating.  I have generated own 
..itp files for the polymer and the simulation is going
ok. But, whenever, I am trying to use g_rdf tool to
calculate the structure factor, it returns the
following error:

Reading frames from gro file '', 89600 atoms.
Reading frame       0 time    0.000  
Program g_rdf, VERSION 3.3.1
Source code file: gmx_rdf.c, line: 819

Fatal error:

Error: atom type (NH3) not in list (18 types checked)!

The command line I am using is as follows:
g_rdf -f conf.gro -n index.ndx -o rdf2.xvg -sq sq.xvg
-s topol.tpr

If I only try to calculate the rdf, it goes fine. But
only when I am using -sq option , I am getting the
error. I checked with gromacs mailing list and I saw
an email having similar problem as mine but I did not
find any solution. It will be great, if  any one can
help me with this problem.

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