Hi,
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.
Thanks
Jagannath
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