[gmx-users] How to get an index file containing non polar atoms in gromacs?

[Catarina A. Carvalheda dos Santos]

I think you can figure this out after playing 5 min with the make_ndx tool,
but here it goes:

"r ILE | r LEU | r VAL" will select all the isoleucines, leucines and
valines in your system.

Cheers,


On 25 January 2016 at 12:23, Shima ebrahimi <sh_ebrahimi at ut.ac.ir> wrote:

>
>
> Dear Users,
>
> I want to determine hydrophobic interaction between ligand and protein
> using g_mindist. However, how can I identify non-polar atoms and specify
> them in the index file.Could anyone help me?
> Regards,
> Shima
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-- 
Catarina A. Carvalheda

PhD Student
Computational Biology Division
SSE & SLS
University of Dundee
DD1 5EH, Dundee, Scotland, UK