Re: [AMBER] Hydrogen bond analysis problem

From: Daniel Roe <>
Date: Fri, 20 Sep 2013 09:50:09 -0600


On Fri, Sep 20, 2013 at 3:04 AM, Sumra Wajid Abbasi 30-FBAS/MSBI/F09
<> wrote:
> I tried cpptraj but following error occurred :
> Error: Could not set up file prod_1-8.binpos for reading.
> Error: trajin: Could not set up trajectory.

You need to be using cpptraj from AmberTools 13 to process Binpos
trajectories (in general it's best to upgrade to the latest version of
the code anyway).

> kindly check is it ok secondly can you please tell me know how can i
> visualize results actually i want to generate graph of hydrogen bond
> analysis

If you want to visualize the lifetime analysis you could get
gnuplot-readable output with the 'lifetime' command in cpptraj. For
example, the following input:

parm topology.parm7
hbond H1 series .N,H,C,O
runanalysis lifetime H1[solutehb] out life.5.gnu window 5

will first calculate hydrogen bonds, searching for donors/acceptors in
the provided mask and saving the time series data as H1. Then lifetime
analysis will be run on the solute hydrogen bond time series
(H1[solutehb]) over time windows 5 frames in length. You will end up
with 3 gnuplot-readable files: life.5.gnu will show the lifetimes, will show the max lifetimes, and will
show the average lifetimes.

Hope this helps,


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Fri Sep 20 2013 - 09:00:02 PDT
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