Hi,
The donormask/donorhmask/acceptormask keywords allow users to
fine-tune hydrogen bond selection; as stated in the manual, CPPTRAJ
will accept whatever you specify for these masks as hydrogen bond
donors and acceptors. To give users maximum flexibility, it does this
without double checking what the atoms are. So if you do something
like 'acceptormask *' then _every single atom_ is a potential hydrogen
bond donor. So you may just need to adjust your acceptormask to
exclude hydrogens (although I'm just guessing, not having seen your
input).
-Dan
On Wed, Nov 18, 2020 at 7:43 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>
> Hello users and developers
>
> While running hbond analysis without defining either donors/acceptors the “autodetect” function seemingly identifies pairs rather correctly (not including solvent). However, when running with defined donor/acceptor pairs though not defining donorhmask, there are a lot of instances where it seems that CPPTRAJ has identified a hydrogen forming a hydrogen bond with another hydrogen.
>
> #Acceptor DonorH Donor Frames Frac AvgDist AvgAng
> PHE_7.HE1 APM_12.H7 APM_12.C5 2 0.0002 2.9817 140.9910
>
> I suppose that this is because these atoms fulfilled the criteria of a hydrogen bond with regard to angle and distance. However, unless I am misreading the output, this would indicate a
>
> APM_12.C5 — APM_12.H7 ::: 1EH.7_PHE
>
> Hydrogen bond being formed. For one, C5 would disqualify this as being a HBOND (no N/F/O) and the bond would be between H and H.
>
> I suppose that this is not the correct way to use the definitions?
>
> With a system including X, Y and WAT, what would be the input/masks required to run without defining any donor/acceptor information. Then running donor X vs acceptor Y and donor Y acceptor X?
>
> Best regards
> // Gustaf
>
>
>
>
>
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Received on Wed Nov 18 2020 - 06:30:04 PST
