Conformers analysis

Calculation of properties with Vega

File - Open and select filename_mol_wat_final.mol2

The file mol2 is uploaded in Vega and the "Analysis of the trajectory" window is opened

In the "Analysis of the trajectory" window, select a property and click the ok button, Vega calculates and plots the property

Properties that we usually use

Polar surface area, PSA;
Gyration radius, RGyr;
Molecular Lipophilicity Potentials to calculate the Virtual Log P (less used, ask to the director)

Click on "Save as csv file" to save the results

Finally, export the multimol2 file in pdb format

File - Save trajectory - select pdb format

Import the results in Excel and merge with the energy output of Szybki

Pay attention in the merging to avoid errors
The order of the Vega output MUST be the same of the Szybki output to guarantee the perfect correspondence between energy and property values foreach conformer

Cluster analysis

Cluster analysis is carried out using Chimera software but before the analysis the mol2 output of Omega has to be converted in pdb format by OpenBabel.

Conversion of mol2 to pdb file

In the command window used to run omega use the following command

babel -imol2 mol_oe_sz.mol2 -opdb mol_oe.pdb

Cluster analysis

Launch Chimera.

From menus: Tools - MD/Ensemble Analysis - MD Movie

Trajectory format: PDB

PDB frames contained in single file

Browse and select the pdf file

Finally, click on "Set input location"

Now the conformations are loaded as a trajectory.

From MD Movie Tool window Analysis - Cluster

Cluster based on current selection, if any true

Atoms must not be selected

All Ignore options have to be true and alkali for the last

Save the results in a text file mol_wat_cluster.txt

In the cluster file, conformations are clustered and the first frame represent the most representative conformation of the cluster in terms of geometry criteria. Using the output of Szybki the minimum energy conformer should be find and used for the next steps (Chimera does not calculate any energy values).

Python script to read Chimera cluster output and to write clusters in columns in order to merge with szybki output

file = open("MZ1_wat_cluster_final.csv","r")
fileout = open("MZ1_wat_cluster_final_col.csv","w")
i=0
j=0
for line in file:
    i=0
    fields=line.split(" ")
    indice=len(fields)-1
    for ind in range(indice):
        print (j, fields[i].rstrip())
        fileout.writelines([str(j) + " ; " + fields[i].rstrip() + "\n"])
        i=i+1

    j=j+1