Dear AMBER users,
This is a query from my group member who was (somehow) unable to get into
the AMBER mailing list. Answers appreciated.
Thank you,
Neelanjana Sengupta
Dear List Members,
I am using "hbond" command in cpptraj with the following lines as mentioned
in one of the "hbond Examples" of AMBER-Hub
hbond HB out nhb.dat avgout solute_avg.dat \
solventacceptor :WAT.O solventdonor :WAT \
solvout solvent_avg.dat bridgeout bridge.dat \
series uuseries uuhbonds.agr uvseries uvhbonds.agr
The [series] keyword should save hydrogen bond formed (1.0) or not formed
(0.0) per frame for any detected hydrogen bond.
However, the uvhbonds.agr file (which write solute-solvent hbond time
series data) gave data in many places as 2 and 3.
Could someone please assist me in comprehending these results?
Regards,
--
Rakiba Rohman
Post-doctoral Fellow, DBS
Indian Institute of Science Education and Research (IISER) Kolkata
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Received on Wed Aug 30 2023 - 00:00:02 PDT
