[gmx-users] Re: hydrophobic contacts

[Justin Lemkul]

On 11/14/12 2:27 AM, Raj wrote:
> Hi all,
>
> can some one tel me how can i prepare a index file specifying the
> hydrophobic atoms along for measuring the hydrophobic contacts in the
> systems alone.
>

There is no straightforward way to do this, as far as I know.  I generally 
construct such groups by selecting groups of hydrophobic residues and then parse 
out the hydrophobic atoms within these groups.  You can narrow down your 
selections using default groups like Sidechain (since the protein backbone is 
highly polar) and select by atom type using a .tpr file as the input to make_ndx.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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