Re: [AMBER] About calculating entropy

From: Jason Swails <>
Date: Thu, 31 Oct 2013 09:14:59 -0400

On Thu, Oct 31, 2013 at 7:26 AM, Olayide Arodola

> Hi,
> i need help on how to calculate free binding energy and entropy in one
> script using amber 12. Below is the copy of my input file. i keep getting a
> dat file without any result in it. it will read the input file
> successfully, produce a data for free binding energy but it wont produce
> any data for entropy. please can you tell me how to go about this? is this
> a technical problem or is there something wrong with my input file or is my
> interval too small/ big? please i need an immediate response because i have
> been stuck at this point for the last 2 months and its delaying my
> research. please i need to move forward from here and compute my result.
> Thank you.
> Please check out my input file below:
> Input file for running PB and GB in serial
> &general
> startframe=1, endframe=5000, interval=50, keep_files=0,entropy=1,

Here you are specifying 100 total frames for use with the quasi-harmonic
approximation. In order to use the quasi-harmonic approximation, you need
at least 3N frames, where N is the total number of atoms in your complex.
 Even 5000 frames is unlikely to be enough. Furthermore, it typically
takes a huge number of frames to actually converge a quasi-harmonic entropy
calculation, and based on previous discussions on this list it would not
surprise me if your results did not make much sense.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Oct 31 2013 - 06:30:03 PDT
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