This is a re-message as I got some error during sending
use this input
Input file for running PB and GB in serial
&general
startframe=1, endframe=5000, interval=5,keep_file=0, (please amend frames
accordingly)
/
&gb
igb=5,saltcon=0.15,
/
&decomp
idecomp=1, print_res="561;72;15;219;184;114;110;113;115;116", (yellow
highlighted is the ligand number)
dec_verbose=1,csv_format=0,
Submit the command with this input.. enjoy!!
An example paper of ligand -residue or per residue interaction plot
http://pubs.rsc.org/en/content/articlepdf/2014/mb/c3mb70577c
On Sat, Apr 5, 2014 at 2:39 PM, Jason Swails <jason.swails.gmail.com> wrote:
> Your question was asked and answered close to an hour ago on the mailing
> list. Please check your spam filters to make sure you are getting emails
> to the amber mailing list.
>
> I've answered one of your questions in the text below
>
> On Sat, Apr 5, 2014 at 7:39 AM, Arunima Shilpi <writetoash28.gmail.com
> >wrote:
>
> > Dear Sir
> >
> > Presently I am doing binding free energy decomposition was performed
> based
> > on
> > MM/GBSAdelta and MM/PBSA .
> >
> > I want to plot energy contributions from each residue with the ligand
> thus
> > plotting ligand-residue inteaction scpectra.
>
>
> > Kindly guide me with the command to be used to study the interaction.
> >
>
> It is impossible to prepare a command (script or program) with Amber that
> will do EVERY type of analysis people would want. Analyzing data that is
> generated _from_ an analysis program is typically not the domain of Amber
> programs. For instance, it may be a plotting program like gnuplot,
> xmgrace, or some spreadsheet coupled with either a clever little script you
> wrote or a bit of work copying numbers from one place to another.
>
> To create the plots you want, you can do any number of things -- you can
> copy your data into a spreadsheet (like MS Excel or
> OpenOffice/LibreOffice), you can write a script to postprocess the data and
> put it into a format understood by xmgrace or gnuplot, you can write a
> Python script with the matplotlib library to postprocess and plot in the
> same step, you can do the same in matlab, etc.
>
> Long story short, this step is up to you.
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Thanks & Regards;
Soumendranath Bhakat
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Received on Sat Apr 05 2014 - 09:30:07 PDT
