Dear Amber Community,
I’m getting different results depending on how I ue the hbond analysis feature in CPPTRAJ, and I’d like to understand the origin for the difference.
First, I ran:
hbond All out All.hbvtime.dat solventdonor :WAT solventacceptor :WAT.O \
avgout All.UU.avg.dat solvout All.UV.avg.dat bridgeout All.bridge.avg.dat
This gave, for example:
….
SER_1016.O ALA_1018.H ALA_1018.N 12 0.0322 2.8752 145.8849
…
However, if I run:
hbond donormask :1018 acceptormask :X avgout temp_Res_1018-X_avg.dat
Where “X” is looped over all possible residues, I get two avg.dat files that contain
GLN_1009.HB2 ALA_1018.HA
ALA_1018.CA 10 0.0268 2.9364 140.2398
SER_1016.O ALA_1018.H ALA_1018.N 12 0.0322 2.8752 145.8849
Why did the H-bond to GLN_1009.HB2 not appear in the output from the first command? Do the two commands use different criteria?
Best,
Matthew
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Received on Thu Mar 17 2022 - 09:30:03 PDT
