[gmx-users] RE: query about g_rdf and make_ndx

Mauricio Sica msica at unq.edu.ar
Wed Feb 21 13:41:28 CET 2007

> Dear All,
>...I think I should generate an .ndx file with  all the atoms
> I need as well as the solvent molecules, but I have some basic problem
> in understanding the preparation of .ndx file, when I am executing the
> commnad make_ndx and select system, index file is being prepared, but
> there I can not specify groups , everytime  it is said that group is
> empty, I am doing some mistake , but can not detcet it, please help in
> this two matters.
>   regards

To make a group cosisting in residue 'X' and 'Y' and the group 
"SOL" (group 'Z' in the index file), at the  prompt of command

        'make_ndx -f topol' 

you should type something like: 

        'rX  &| rY &| Y'

And so on

Good luck


Dr. Mauricio P. Sica                    LEPP
Phone: (54011)4365-7100 ext. 169        Laboratorio de Expresión
R. Saenz Peña 354                       y Plegado Proteico
(B1876BXF) Bernal, Buenos Aires         Universidad de Quilmes

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