[AMBER] bond angle and distance calculation

From: Hoshin Kim <85hskim.gmail.com>
Date: Thu, 17 Jun 2010 17:48:18 +0900

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

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.


Hoshin Kim.
Hoshin Kim
Visiting Scholar
Department of Chemical and Biomolecular Engineering
North Carolina State University
Raleigh, NC 27695
Phone: 919-986-9258
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 Thu Jun 17 2010 - 15:00:03 PDT
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