Dear Daniel,
thanks for Your reply. No, I don't want cpptraj to use closer of the two
(or more) distances but to use their r^-6 weighted average. i.e.: to use
r^-6 weighted average of all distances per frame in the mask to compute
their final r^-6 weighted average over the whole trajectory to get NOE
violations. What I get now is r^-6 weighted average over the whole
trajectory computed for center-of-mass distances, not for r^-6 weighted
averages (per frame). This leads to slightly higher values of NOE
violations for multiple-mask distances with "distance type noe" than what
is the correct value. Sander can be also used to analyze NOE violations and
there the r^-6 weighted averaging for multiple-atom NOEs works well.
Best wishes,
Pavlina
On Wed, Nov 25, 2020 at 4:26 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Sorry for the long delay on this. So do you mean you want cpptraj to
> automatically choose the closer of the two distances? If so, you can't
> do that with the 'distance' command, but you might be able to get it
> to work with the 'nativecontacts' command and the 'mindist' keyword.
> The generated dataset with the [mindist] aspect could then be sent to
> the 'stat' analysis. Disclaimer: I haven't had a chance to test it,
> but that seems like it should work with those atom masks.
>
> -Dan
>
> On Mon, Oct 19, 2020 at 9:18 AM Pavlína Pokorná <pokorna.pavlina.ibp.cz>
> wrote:
> >
> > Dear all,
> >
> > I have a question regarding NOE analysis when using a multiple-atom mask
> > with cpptraj.
> >
> > If I use:
> > distance 117RADE_H8-41LYS_QG :117.H8 :41.HG= type noe noe_weak
> > analyze statistics all out noe.dat noeout noeout.dat
> >
> > --> cpptraj then uses center-of-mass of :41.HG2 and :41.HG3 atoms to
> > compute its r6 weighted average distance with :117.H8 instead of
> treating
> > each of the :41.HG* atoms individually. There is no problem if I
> calculate
> > NOE with equivalent command using masks which both contain only one
> > hydrogen atom.
> >
> > So, is it possible to make cpptraj use the r6 weighted averaging instead
> of
> > center-of-mass averaging when "type noe" is specified for distance action
> > with multiple atoms in the mask? Did I miss something with my cpptraj
> > commands?
> >
> > Thank You,
> > Pavlina Pokorna
> >
> >
> > --
> > RNDr. Pavlína Pokorná
> > *PhD student*
> > Institute of Biophysics of the CAS, v. v. i.
> > Kralovopolska 135, 612 65 Brno
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--
*RNDr. Pavlína Pokorná*
*PhD student*
Institute of Biophysics of the CAS, v. v. i.
Kralovopolska 135, 612 65 Brno
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Received on Wed Dec 02 2020 - 04:30:02 PST
