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MD Simulation Step by Step

The document outlines the steps for conducting molecular dynamics simulations using Maestro software, including protein preparation, simulation environment setup, and running the simulation. It details the specific commands and parameters needed for tasks such as defining ligands, preparing the protein complex, and analyzing simulation results. The final output includes various metrics related to protein-ligand interactions and structural stability.

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caro leeja
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56 views3 pages

MD Simulation Step by Step

The document outlines the steps for conducting molecular dynamics simulations using Maestro software, including protein preparation, simulation environment setup, and running the simulation. It details the specific commands and parameters needed for tasks such as defining ligands, preparing the protein complex, and analyzing simulation results. The final output includes various metrics related to protein-ligand interactions and structural stability.

Uploaded by

caro leeja
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as TXT, PDF, TXT or read online on Scribd
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maestro ver 11.5.

011

18 demo md simulation sid analysis (manipal schrondiger) - youtube (51:25)


10.1016/j.jmgm.2019.07.002 - in silico analysis of bacteriophage tail tubular
proteins suggests a putative sugar binding site and a catalytic mechanism

Open terminal
cd /home/sbls/Desktop/softwares/Schrodinger_Suites_2018-1_Linux-x86_64/2024
Type “./maestro”

1. prepare protein complex


file - change working directory - [file name]
file - save project as [simulation]
file - get pdb
File > import structure > select protein complex > Open

define ligand
at the bottom right click on the plus sign
select command input area
type 'set ligand chain.name A, D

or

define tab
chain
select chain name
add
okay

Protein preparation wizard > Import and Process


Select the following option
- Assign bond orders
• Use CCD database
• Add hydrogen
• Create zero-order bonds to metals
• Create disulfide bonds
• Fill in missing side chains using prime
• Delete waters beyond 5.00 Å from het groups
- Generate het states using Epik: pH 7.0 +/- 2.0

Click Preprocess.
Go to refine option
select the following
sample water orientations
using PROKA pH 7.0 - optimise
Remove waters beyond hets 3.0 Å - remove water
Restrained minimization force field: OPLS3e - minimise

2. create Simulation Environment


Task > Browse > Desmond > System Builder

Select the following Solvation parameters


• Predefined: Spc
• Box Shape: Orthorombic
• Box Size Calculation Method: Buffer
• Distance (Å): 10x10x10
• Box volume: Default
• Show boundary box
• Minimize volume
• Force Field: OPLS3e

Select the following Ions parameters


• Neutralize by adding ions: Default
• Add Salt
salt conc 0.15m
Click the “run” option.

3. How to Run the Molecular Dynamic Simulation


• Task > Browse > Desmond > Molecular Dynamics
- load from workspace
• Select the “Load” option
• System is loaded
xxx It contains 126363 atoms

Choose the proper simulation time


• simulation time - 10ns
recording interval- 10
approx number of frames - 1000
energy 10
ensemble class - npat (normal pressure area and temp )
temp - 300
pessuer 1.01325
relax mode checked

advanced setting s- leave as default

run

4. task - browse - desmond - simulation interaction diagram


load - md job
protein - auto
ligand - auto
Frame - 0
analysis type - select all

run

view protein ligand RMSD (root mean square deviation)


- the protein should not unbind from the ligand

5. file has a .eaf (event analysis file)

in the file you will get the following


1. PL-RMSD - protein ligand root mean square deviation
2. P-SSE - protein secondary structure
3. P--RMSF - protein root mean squar fluctuation
4. L-RMSF - ligand root mean squar fluctuation
5. PL-Contacts - protein ligand contact
6.

5740 - desmond md job 5740 - contains 126363 atoms/ 2nd time 126581 (26th march
2025)
5791 - 25965 atoms
xxxxxxxxxxxxxxxxxxxxxx
steps
added hydrogens
optimisedd the hydrogens
removed water molecules
minimised the structure to make sure there are no clashes

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