Re: [AMBER] Would liek to plot GBTOT vs Time

From: Jason Swails <jason.swails.gmail.com>
Date: Mon, 14 Mar 2011 00:02:28 -0700

If you used MMPBSA.py, then it creates complex, receptor, and ligand files
should be named _MMPBSA_complex_gb.mdout, _MMPBSA_receptor_gb.mdout, and
_MMPBSA_ligand_gb.mdout. I've written a script (attached here) that
extracts all of the energy components and puts it into files. It will only
work for these files though (or other mdout files with the same names).

In it, I use awk and grep similar to Dan's suggestions. Hopefully it can
serve as a template to help you learn scripting to some extent, as efficient
scripting definitely helps bolster productivity.

Hope this helps,
Jason

On Sun, Mar 13, 2011 at 10:59 PM, Mannan <malie_03.yahoo.co.in> wrote:

> Hi Amber ppls,
>
> I would like to plot the GBTOT vs Time,
> I do have all the data (Com,Rec and Lig)to combine,
>
> But I am looking for a script to do that, I am not well versed with
> scripts,
> Adding VDWAALS, 1-4 VDW |||ly
>
> Is there any webserver, where I would get the same.
>
>
> Thanks in Advance,
> Mannan.
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032



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Received on Mon Mar 14 2011 - 00:30:02 PDT
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