Re: [AMBER] NOE analysis with cpptraj

From: Daniel Roe <>
Date: Wed, 25 Nov 2020 10:24:11 -0500


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.


On Mon, Oct 19, 2020 at 9:18 AM Pavlína Pokorná <> 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
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Wed Nov 25 2020 - 07:30:04 PST
Custom Search