Dear Jason,
Thank you for your response and advaise to use MMPBSA.py.
I have observed that ligand fluctuates between several different orientations in the receptor active site.
I need to identify the average 3D structures of these conformational clusters of the ligand.
That is why I want to analyse the energetic profile of receptor-ligand complex depending
on different orientations of the ligand accepted during productive MD trajectory.
For the analysis I need to eliminate a big energetic noise produced by bulk solvent water molecules.
I am not sure, unfortunately, that the MMPBSA.py is a relevant option in my case,
since it is impossible to applay MMPBSA.py for the analysis of md.mdcrd trajectory file
generated on 25000 frames of productive MD.
I would appreciate your advice that could be applied for my task.
Thank you,
Michael
*****************************
Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
Israel
email: shokhen.mail.biu.ac.il
________________________________________
From: Jason Swails <jason.swails.gmail.com>
Sent: Sunday, February 14, 2016 2:14 PM
To: AMBER Mailing List
Subject: Re: [AMBER] summary.ETOT analysis
> On Feb 14, 2016, at 4:47 AM, Michael Shokhen <michael.shokhen.biu.ac.il> wrote:
>
> Dear Amber list experts,
>
> I have MD simulated in Amber14 complex of enzyme with non covalent inhibitor.
> The simulation was conducted in octahedral periodic cell with explicit water molecules
> and counter ions.
> I used a standard command for the analysis of total energy of the whole system along
> the productive MD trajectory (summary.ETOT):
>
>
> cd analysis_md3-md8
> nohup perl $AMBERHOME/AmberTools/src/etc/process_mdout.perl ../5_/md3.out ../6_/md4.out ../7_/md5.out ../8_/md6.out ../9_/md7.out ../10_/md8.out &
>
> My question is: How should I modify the command in order to calculate the summary.ETOT
> of protein + ligand complex and also separately summary.ETOT (enzyme) and
> summary.ETOT (ligand) only, without energy contribution of water and counter ions?
process_mdout.pl doesn't calculate anything. All it does is parse numbers from mdout files. So there is no way to have process_mdout extract the numbers you want.
This is what programs like MMPBSA.py are designed for.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Feb 14 2016 - 05:30:03 PST
