[AMBER] hbond cpptraj

From: Jon Uranga <jonur9.gmail.com>
Date: Mon, 15 Mar 2021 14:47:17 +0100

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

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!



Jon Uranga
Institute of Physical Chemistry
Computational Chemistry and Biochemistry Group
Tammannstr. 6
37077 Göttingen
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
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