Hello Daniel,
Thanks for the detailed reply. I wonder about the possibility of using
'resseries present' with 'savenonnative' or 'skipnative' to get 1 to 1
contact map. The 'resseries present' in nativecontacts can get the time
series contact matrix of 1 and 0 for each residue pair. I wonder the
possibility of using CPPTRAJ to get an average (over the frames) of the
'resseries present' output as the output matrix contain contact details for
each frame and this frame-averaged matrix can be then visualized. Let me
know what you think and how I can use the CPPTRAJ to achieve this?
Many thanks in advance
Best
Anu
On Thu, May 2, 2019 at 8:25 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> You can get a combined contacts map by just considering every contact
> to be "non-native" using the 'skipnative' keyword; this keyword is
> relatively new so use the GitHub version of cpptraj.
>
> Normalizing it to 1 is a little more problematic. The way cpptraj
> normalizes by-residue contacts is a little strange - the final values
> currently reflect how many potential contacts a residue can make (so
> e.g. TRP residues can end up with higher values than GLY residues). To
> do a 1 to 1 map you could either to a C-alpha contacts map (while
> increasing the default distance cutoff), or create a pseudo trajectory
> of each side chain center of mass (via 'vector' and 'writedata
> vectraj'), then dot he native contacts analysis on the pseudo
> trajectory (more details in the manual). Let me know if you have more
> questions.
>
> Hope this helps,
>
> -Dan
>
> On Wed, May 1, 2019 at 3:06 PM anu chandra <anu80125.gmail.com> wrote:
> >
> > Hello Amber users,
> >
> > I am trying to generate an average residue-wise contact map along the
> > simulation time. Using nativecontacts in CPPTRAJ, I could generate native
> > and nonnative contact map as well as residue time series contact.
> However,
> > I wonder whether it is possible to get an average residue-wise contact
> map
> > matrix (where 1 for contact and 0 for no contact), using CPPTARJ, that
> > contain sum of both native and nonnative contacts?
> >
> >
> > Any help would be appreciated.
> >
> > Best regards
> > Anu
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Received on Thu May 02 2019 - 09:00:02 PDT
