Hi,
On Thu, Oct 15, 2020 at 3:53 PM German P. Barletta <pbarletta.gmail.com> wrote:
> The amber manual says cpptraj follows this simple criterion:
>
> *"...hydrogen bonds are FON”, i.e., hydrogens bonded to F, O, and N atoms
> are considered donors, and F, O, and N atoms are considered acceptors.". *
You omitted the first part of that sentence which is actually very
important (asterisk emphasis mine):
'*Automatic determination* of hydrogen bond donors/acceptors uses the
simplistic criterion that “hydrogen bonds are
FON”,'
So that criterion is only in effect for cases where 'donormask' and
'acceptormask' are *not* specified; there is a list of 4 keyword use
cases just preceding that sentence that make this clear. The
'donormask' and 'acceptormask' keywords are so users can fine-tune the
atoms considered for hydrogen bonding if they wish (to look for e.g.
halogen bonds), so they assume the mask you give them contains all the
atoms you want. If you want to restrict to F, O, and N atoms you will
need to be explicit, e.g.
hbond acceptormask :4./F,O,N ...
Hopefully this clarifies things,
-Dan
>
> So, why am I getting these results?
>
> I know I could just add the atom elements to the *acceptormask*, but I was
> wondering why this happens.
>
> Best,
> Germán P. Barletta
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Received on Thu Oct 15 2020 - 16:00:02 PDT
