Dear Amber users,
I am writing with regard to the hbond command of cpptraj (V18.01). I am
trying to analyze the H bond interaction between several
hydrophilic residues in an enzyme and among all these interactions one is
between a glutamine (residue number 358) and an aspartate (residue number
350). Since there are plenty of interactions and I am only interested in
the H bond between different residues I have included 'nointramol'.
However, I am experiencing something unexpected which I would like to ask
herein.
In case that 'nointramol' is present, I do not get the interaction between
the glutamine and the aspartate:
*hbond inter out hbond.dat donormask :358.NE2 acceptormask :350.OD2
nointramol avgout hbond.av*
However, if I remove 'nointramol', now I do get the value corresponding for
this interaction.
Since this interaction is intermolecular I cannot understand this
behaviour. Is there something wrong in the command I have written here?
Thanks a lot!
Bests,
Jon
--
*********************************************************
Jon Uranga
Institute of Physical Chemistry
Computational Chemistry and Biochemistry Group
Tammannstr. 6
37077 Göttingen
Germany
Office Phone: 33131
E-mail: jon.uranga.chemie.uni-goettingen.de
*********************************************************
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Received on Mon Mar 15 2021 - 07:00:02 PDT
