Conformational Sampling (Vega)

Introduction

Conformational sampling performed with Vega.

Data input

Input

Launch Vega

File - Open - Choose the file (generally a mol2 file)

Assign charges and potential.

Calculate - Charge & Pot

Choose parameters:

• FF: SP4
• Charges: Ammp-Mom

Then, click Fix.

• Check the total charge.

Finally, minimize the structure to be sure that all is ok.

Calculate - Ammp - Run

• Use default parameters
• Save the file in the working directory: File - Save as

Conformational sampling

Setup the simulation

Calculate - Ammp - Run - Conformational search

In the Conformational search window select the different panels clicking on the label on the bottom to setup the simulation:

• Conformational search panel
• Method: Boltzman jump (default)
• Default parameters
• Set the torsion angles
• Edit torsion - Edit - Add torsion - Flexible
• Output panel
• Click to save Trajectory, Output and Energy
• Check that files are saved in the working directory
• Parameters
• Dielectric Constant: 80.0/4.81 wat(ca)/chl(ne)
• Potential
• Type: SP4

Finally, click Run

Analyses of the trajectory

Calculate - Analysis

• Select the Trajectory that was saved in dcd format and then calculate properties (e.g. RGyr and 3D-PSA)