[gmx-users] Re: hydrophobic contacts
jalemkul at vt.edu
Wed Nov 14 13:23:57 CET 2012
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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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