On Thu, Oct 31, 2013 at 7:26 AM, Olayide Arodola
<olayide.arodola.gmail.com>wrote:
> 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.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Oct 31 2013 - 06:30:03 PDT
