`g_mmpbsa correlation`

It performs same operation as g_mmpbsa average but also calculates correlation between predicted and experimental binding energies. It used the same input files as g_mmpbsa average with the additional file containing experimental binding free energies.

It also fits a straight line to the data and calculates the correlation coefficient (R).

Command summary

g_mmpbsa correlation [-h] [-mt] [-mf metafile.dat] [-m energy_MM.xvg] [-p polar.xvg]
                     [-a apolar.xvg] [-bs] [-nbs NBSTEP] [-of full_energy.dat]
                     [-os summary_energy.dat] [-om meta_energy.dat]
                     [-ep enplot.png] [-cd corrdist.dat] [-cp corrdist.png]

Description

`-mt, --multiple`

If given, calculate for multiple complexes. Need Metafile containing path of energy files

`-mf metafile.dat, --metafile metafile.dat`

Metafile containing path to energy files of each complex in a row obtained from g_mmpbsa in following order: [MM file] [Polar file] [ Non-polar file] [Ki] Ki Should be in NanoMolar (nM)

`-m energy_MM.xvg, --molmech energy_MM.xvg`

Vacuum Molecular Mechanics energy file obtained from g_mmpbsa

`-p polar.xvg, --polar polar.xvg`

Polar solvation energy file obtained from g_mmpbsa

`-a apolar.xvg, --apolar apolar.xvg`

Non-Polar solvation energy file obtained from g_mmpbsa

`-bs, --bootstrap`

If given, Enable Boot Strap analysis

`-nbs NBSTEP, --nbstep NBSTEP`

Number of boot strap steps for average energy calculation

`-of full_energy.dat, --outfr full_energy.dat`

Energy File: Energy components frame wise

`-os summary_energy.dat, --outsum summary_energy.dat`

Final Energy File: Full Summary of energy components

`-om meta_energy.dat, --outmeta meta_energy.dat`

Final Energy File for Multiple Complexes: Complex wise final binding nergy

`-ep enplot.png, --enplot enplot.png`

Experimental Energy vs Calculated Energy Correlation Plot

`-cd corrdist.dat, --corrdist corrdist.dat`

Correlation distribution data from bootstrapping

`-cp corrdist.png, --corrplot corrdist.png`

Plot of correlation distribution

g_mmpbsa correlation

Command summary

Description

-mt, --multiple

-mf metafile.dat, --metafile metafile.dat

-m energy_MM.xvg, --molmech energy_MM.xvg

-p polar.xvg, --polar polar.xvg

-a apolar.xvg, --apolar apolar.xvg

-bs, --bootstrap

-nbs NBSTEP, --nbstep NBSTEP

-of full_energy.dat, --outfr full_energy.dat

-os summary_energy.dat, --outsum summary_energy.dat

-om meta_energy.dat, --outmeta meta_energy.dat

-ep enplot.png, --enplot enplot.png

-cd corrdist.dat, --corrdist corrdist.dat

-cp corrdist.png, --corrplot corrdist.png