I’m gate crushing into the discussion as I have had to deal with a similar situation as that described by Michael.
The way I dealt with such problem (if I understood Michael’s problem correctly) is to use cpptraj clustering, which generates trajectories of individual clusters and then apply MMPBSA.py to each cluster (at least the most populated ones). Alternatively, MMPBSA.py could be applied (I think) to pseudo trajectories generated by cpptraj PCA analysis.
Apologies, in advance, if I am way off the mark.
Regards
George
> On 14 Feb 2016, at 14:10, Michael Shokhen <michael.shokhen.biu.ac.il> wrote:
>
> 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 - 07:30:03 PST
