Re: [AMBER] Clustering using CPPTRAJ

From: Jason Swails <>
Date: Mon, 23 Jun 2014 11:19:04 -0400

On Mon, 2014-06-23 at 16:45 +0200, Soumendranath Bhakat wrote:
> Dear Dan;
> Say I want to calculate both GBSA and PBSA calculations on these filtered
> frames. How the script should be and how can I know which is starting frame
> and which is end frame?

The start frame and end frame correspond to the frame numbers of the
input trajectories (frames are numbered from 1 to N in the order that
the trajectories are specified in).

> Below a prototype script to run parallel PBSA and GBSA. How can I know
> frame numbers that will be filtered?

The input file below will use frames 1 through 50, inclusive. The
filtering variables are: startframe, endframe, interval. The frames
analyzed will be startframe, startframe+interval, startframe
+2*interval, ..., startframe+N*interval for all frames less than or
equal to endframe.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Jun 23 2014 - 08:30:03 PDT
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