Hi,
On Wed, Mar 29, 2017 at 12:34 PM, Andreas Tosstorff
<andreas.tosstorff.cup.uni-muenchen.de> wrote:
>
> 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?
The terms 'most probable' and 'stable' are typically associated with
'lowest free energy'. Whether or not you can extract this from your
simulation depends entirely on how well you have sampled your system's
conformational space (at least if you plan on doing it via
population). One of the best ways to do that is to compare at least
two (but ideally multiple) independent simulations that start from
different conformations and determine how well-converged they are. For
some examples of this that use cpptraj see:
http://rnajournal.cshlp.org/content/21/9/1578.short
http://www.sciencedirect.com/science/article/pii/S0304416514003092
http://pubs.acs.org/doi/abs/10.1021/jp4125099
http://pubs.acs.org/doi/abs/10.1021/ct400862k
If you don't have a converged trajectory you can still figure out what
conformations are most populated in your simulation via cluster
analysis, but you probably won't be able to determine if they are the
most stable without further simulation or a different approach. Hope
this helps,
-Dan
>
>
> 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
>
> --
> M.Sc. Andreas Tosstorff
> Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
> Department Pharmazie
> LMU München
> Butenandtstr. 5-13 ( Haus B)
> 81377 München
> Germany
> Tel.: +49 89 2180 77059
>
>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Thu Mar 30 2017 - 05:30:05 PDT
