> 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 - 04:30:03 PST
