Dear, Amber user
First, I'm beginner of AMBER
I would like to calculate the O-H-O cut-off bond angle and distance between
glucose and trifluoromethylsulfonate(Emim) ion to know H-Bond energy by
using PTRAJ hbond command.
How can I calculate these values in AMBER ?
I have already finished 5ns simulation consisting of glucose as a solute and
Emim as a solvent. So I would like to calcultate these values by extracting
a single conformation of one glucose unit bonded with one Emim anion. Is it
possible ? If not, do I make a new single unit complexed by anion for
calculation?
Thanks in advance and I would appreciate it a lot, if someone give me or
show me sample input file for calculating angle and parameter.
Regards,
Hoshin Kim.
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Hoshin Kim
Now)
Visiting Scholar
Department of Chemical and Biomolecular Engineering
North Carolina State University
Raleigh, NC 27695
Phone: 919-986-9258
Also)
Graduate student (M.D. candidate)
Ionic Liquids Team(ILs) in Bio Nano Process Lab
Department of Biological Engineering,
2S 113, Engineering building Inha University,
253 Yonghyeon Dong, Nam Ku
Incheon, KOREA
TEL) +82-32-860-8655
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Received on Fri Jun 18 2010 - 11:00:03 PDT
