[AMBER] cpptraj donor/acceptor definitions

From: Gustaf Olsson <gustaf.olsson.lnu.se>
Date: Wed, 18 Nov 2020 12:42:45 +0000

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 - 05:00:04 PST
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