My relatively uninformed approach would be to RMS fit one entity to
itself as a reference point, and watch the resulting trajectory for
inspiration while running some sort of cluster analysis on it, which I
think cpptraj has.
Bill
On 3/29/17 9:34 AM, Andreas Tosstorff wrote:
> Hi all,
>
>
> I ran a 500ns simulation to study the dimerization of a peptide and now
> I'm looking into what type of information I can get out.
>
> So far I've been looking into cpptraj's hbond, lie and surf commands.
>
> Is there a possibility to extract somehow the most probable or stable
> dimer structure and to find out which interactions are the most
> important ones for the dimerization to occur?
>
>
> Do you know any other interesting data I can extract from this?
>
> This is completely new to me so I would really appreciate some advice!
>
> Best,
>
> Andy
>
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Received on Wed Mar 29 2017 - 10:00:03 PDT
