Unable to calculate solvent density around a protein #4628
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Rabiul-MDanalysis
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Hello everyone,
I am trying to calculate the solvent density around a protein with MDAnalysis. I followed this tutorial: https://userguide.mdanalysis.org/stable/examples/analysis/volumetric/density_analysis.html
I have used the following code:
import MDAnalysis as mda
from MDAnalysis.tests.datafiles import PSF, DCD
from MDAnalysis.analysis import density
import numpy as np
import matplotlib.pyplot as plt
import nglview as nv
u = mda.Universe('sars_ETO_WAT_CLA_final.psf', 'sars_ethanol_prod_1.dcd')
from MDAnalysis import transformations as trans
protein = u.select_atoms('protein')
water = u.select_atoms('resname TIP3')
workflow = [trans.unwrap(u.atoms),trans.center_in_box(protein, center='geometry'),
trans.wrap(water, compound='residues'), trans.fit_rot_trans(protein, protein, weights='mass'),]
u.trajectory.add_transformations(*workflow)
OH2 = u.select_atoms('name OH2')
dens = density.DensityAnalysis(OH2,delta=4.0,padding=2)
dens.run()
But I did not get any output file from where I can get the information about density. I am very much new to MDAnalysis.
Please help me in this regard so that I can calculate solvent density of my protein system.
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