Hi,
On Thu, Oct 13, 2016 at 9:57 AM, George Tzotzos <gtzotzos.me.com> wrote:
> I’d be grateful for any clarifications on the following:
>
> 1. Given the nativecontacts output below
> Read 4000 frames and processed 4000 frames.
> CONTACTS: NC1
> #Res1 #Res2 TotalFrac Contacts
> 123 127 0.5385 16
>
> Am I right to interpret that contacts between Res1(123) and Res2(127) are observed for ~54% of the total number of frames (4000)?
From the Amber 16 manual (29.9.49. nativecontacts):
"#Res1 #Res2 TotalFrac Contacts
Where #Res1 is the first residue number, #Res2 is the second residue
number, TotalFrac is the total fraction of contacts for the residue
pair, and Contacts is the total number of native contacts involved
with the residue pair. Since TotalFrac is calculated for each pair as
the sum of each contact involving that pair divided by the total
number of frames, it is possible to have TotalFrac values greater than
1 if the residue pair includes more than 1 native contact."
In other words, if there are 2 native contacts between residues X and
Y that are always present, the TotalFrac will be 2.0.
>
> 2. How are nativecontacts defined? I’ve looked at he manual but couldn’t find a definition. Am I right to assume that nativecontacts include vdW and electrostatic interactions?
Again from the Amber 16 manual:
"Define and track “native” contacts as determined by a simple distance
cut-off, i.e. any atoms which are closer than <cut> in the specified
reference frame (the first frame if no reference specified) are
considered a native contact."
So it is a simple distance-based cutoff. Hope this helps,
-Dan
>
> Regards
>
> George
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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 Oct 13 2016 - 07:30:03 PDT
