[gmx-users] Intra-protein hydrophobic contacts

[Justin Lemkul]

On 2/12/13 11:29 AM, Kavyashree M wrote:
> Dear Users,
>
> How can intra-protein hydrophobic contacts be found
> for a trajectory. Most of the mails regarding this in the
> list is regarding hydrophobic contacts between chains
> or ligand and protein. So kindly help.
>

Create a group of hydrophobic atoms and choose that group at both prompts with 
g_mindist -on.

-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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