Hi,
If you're talking about the 'nativecontacts' command from cpptraj, it
is described in the Amber manual (page 626 for version 17). Briefly,
it uses a simple distance-based cutoff and reference structure to
assign "native" contacts. The reference for cpptraj is:
Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ:
Software for Processing and Analysis of Molecular Dynamics Trajectory
Data". J. Chem. Theory Comput., 2013, 9 (7), pp 3084-3095.
-Dan
On Mon, Jun 12, 2017 at 12:27 PM, Julio Dominguez <acheron24.hotmail.com> wrote:
> Good day everyone,
>
>
> I was looking for the precise way that native contacts are calculated, I looked in the manual as well as the mailing list but nothing.
>
> I found two references:
>
>
> Best, Robbert B., et al. "Native contacts determine protein folding mechanisms in atomistic simulations." (2013)
>
>
> C. Hardin et al. "Backbone dynamics, fast folding, and secondary structure formation in helical proteins and peptides." (1999)
>
>
> The formulas are different I am not sure which one, if at all, are used in ambertools.
>
>
> Best regards.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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 Mon Jun 12 2017 - 10:30:03 PDT
