On Fri, Feb 6, 2015 at 5:49 PM, Kenneth Huang <kennethneltharion.gmail.com>
wrote:
> James,
>
> I'm honestly not sure- you might be able to write a program to strip out
> the extraneous sections, but I don't know of any other methods available.
> If there is, someone else might be able to point you in the right
> direction.
>
> The only way I know how to consistently get dG as the last column is to
> have it print decomposition for all the residues. Otherwise, the solution I
> tend to use to just manually edit each entry one at a time into a new
> formatted table, which I can imagine is a tedious endeavor the more
> residues you print out.
>
There are a couple approaches here.
1. You can save the decomposition output file to a CSV-formatted file which
is easily read by most data analysis programs/libraries (such as common
spreadsheets, the R programming language, and numerical processing/data
munging Python libraries like pandas and numpy).
2. You can use the MMPBSA.py Python API to write a script and extract
decomposition energies in a nested Python dictionary. These are described
in detail (i.e., which keys point to which objects) in the Amber 14 manual.
3. Write your own script (Python, Perl, sed/awk/grep, tcl, etc.) to do it.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Feb 06 2015 - 17:30:02 PST
