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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Received on Mon Oct 19 2020 - 06:30:03 PDT
