Simulation Process in DESMOND Software How to Open the DESMOND • Open terminal • Type “cd /opt/schrodinger2020-1/” • Press Enter • Type “./maestro” • It might take some time to open the DESMOND depends on your computer hardware configuration 1. How to Prepare the Protein Complex • File > import structure > select protein complex > Open • 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 • Delete waters beyond 5.00 Å from het groups Click Preprocess. (I n Desmond academic version you can’t pre • Go to refine option Select the following option • Generate het states using Epik: pH 7.0 +/- 2.0 • Optimize H bond by using PROKA pH and sample water orientations • Remove waters beyond hets 3.0 Å • Restrained minimization by using force field: OPLS3e 2. How to 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 • Angles(°): 90:90:90 • Box volume: Default • Show boundary box • Minimize volume • Force Field: OPLS3e Select the following Ions parameters • Neutralize by adding ions: Default • Add Salt Click the “run” option. Simulation System building is completed !!! 3. How to Run the Molecular Dynamic Simulation • Task > Browse > Desmond > Molecular Dynamics • Select the “Load” option • System is loaded • It contains 34280 atoms • Choose the proper simulation time • I am running 1 ns simulation now. • You can change recording interval and approx number of frame • I select GPU for run the simulation • Choose the other parameters for your research hypothesis • Click the “run” option Now My MD simulation is running I can check my simulation condition from jobs option Let’s see….. My simulation is running I will get 567.382 ns simulation per day. It will take some time to complete the simulation it depends on your computer hardware. I use RTX 3080 to run this simulation. Simulation is finished. Let’s see the trajectory The simulation take 8 steps to complete 4. Simulation Step Process (8 stages in total) • Summary of user stages: • stage 1 - task • stage 2 - simulate, Brownian Dynamics NVT, T = 10 K, small timesteps, and restraints on solute heavy atoms, 100ps • stage 3 - simulate, NVT, T = 10 K, small timesteps, and restraints on solute heavy atoms, 12ps • stage 4 - simulate, NPT, T = 10 K, and restraints on solute heavy atoms, 12ps • stage 5 - solvate_pocket • stage 6 - simulate, NPT and restraints on solute heavy atoms, 12ps • stage 7 - simulate, NPT and no restraints, 24ps • stage 8 - simulate Thanks for watching and stay with BioSol Centre. Any kind of problem to run simulation on desmond please contact with BioSol Centre biosolcentre@gmail.com Thank you.
Dear Sir or Madam, I am trying to follow your instruction. However, I can not start the job because I can not select a GPU host. The error is cannot start job with dummy GPU host set. Please set a valid CPU or GPU host". Could you please help me with this issue? Many thanks.
a very informative videos and very clear thank you so much for such kind of platform .... i would request you to please make some videos on docking on MOE please
How to perform HB analysis in Desmond? there are 2 atom subsets that i have to choose. I have tried to create a set for atom subset 1, one amino acid, and for atom subset 2: other amino acids. However, it failed to work. Thank you!
Sir plz guide about selection of local host as the software says to activate GPU before running simulation. kindly tell the process to solve this problem
Hi Sir, Whenever i started any job in protein preparation step, it is not updated or incorporated in workspace. so because of that i am not able to perform simulation. Please help me to resolve the issue
Dear Sir or Madam, I am trying to follow your instruction. However, I can not start the job because I can not select a GPU host. The error is cannot start job with dummy GPU host set. Please set a valid CPU or GPU host". Could you please help me with this issue? Many thanks.
Thanks for your enlightening tutorial but I am facing a problem with desmond desmond can't find any GPU on my system, but I have an RTX 3060 graphics what should I do?
Simulation Process in DESMOND Software
How to Open the DESMOND
• Open terminal
• Type “cd /opt/schrodinger2020-1/”
• Press Enter
• Type “./maestro”
• It might take some time to open the DESMOND depends on your computer hardware configuration
1. How to Prepare the Protein Complex
• File > import structure > select protein complex > Open
• 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
• Delete waters beyond 5.00 Å from het groups
Click Preprocess. (I n Desmond academic version you can’t pre
• Go to refine option
Select the following option
• Generate het states using Epik: pH 7.0 +/- 2.0
• Optimize H bond by using PROKA pH and sample water orientations
• Remove waters beyond hets 3.0 Å
• Restrained minimization by using force field: OPLS3e
2. How to 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
• Angles(°): 90:90:90
• Box volume: Default
• Show boundary box
• Minimize volume
• Force Field: OPLS3e
Select the following Ions parameters
• Neutralize by adding ions: Default
• Add Salt
Click the “run” option.
Simulation System building is completed !!!
3. How to Run the Molecular Dynamic Simulation
• Task > Browse > Desmond > Molecular Dynamics
• Select the “Load” option
• System is loaded
• It contains 34280 atoms
• Choose the proper simulation time
• I am running 1 ns simulation now.
• You can change recording interval and approx number of frame
• I select GPU for run the simulation
• Choose the other parameters for your research hypothesis
• Click the “run” option
Now My MD simulation is running
I can check my simulation condition from jobs option
Let’s see…..
My simulation is running
I will get 567.382 ns simulation per day.
It will take some time to complete the simulation it depends on your computer hardware. I use RTX 3080 to run this simulation.
Simulation is finished.
Let’s see the trajectory
The simulation take 8 steps to complete
4. Simulation Step Process (8 stages in total)
• Summary of user stages:
• stage 1 - task
• stage 2 - simulate, Brownian Dynamics NVT, T = 10 K, small timesteps, and restraints on solute heavy atoms, 100ps
• stage 3 - simulate, NVT, T = 10 K, small timesteps, and restraints on solute heavy atoms, 12ps
• stage 4 - simulate, NPT, T = 10 K, and restraints on solute heavy atoms, 12ps
• stage 5 - solvate_pocket
• stage 6 - simulate, NPT and restraints on solute heavy atoms, 12ps
• stage 7 - simulate, NPT and no restraints, 24ps
• stage 8 - simulate
Thanks for watching and stay with BioSol Centre.
Any kind of problem to run simulation on desmond please contact with BioSol Centre
biosolcentre@gmail.com
Thank you.
Dear Sir or Madam, I am trying to follow your instruction. However, I can not start the job because I can not select a GPU host. The error is cannot start job with dummy GPU host set. Please set a valid CPU or GPU host". Could you please help me with this issue? Many thanks.
Very helpful video dada....love from Kolkata
Very enlightening video,,, it will help those guys tremendously who are hungry for research.
Thanks for supporting us.
Yes you are right. I would say they should think more about theoretical part first and go further. I appreciate their overall effort though.
Very Impressive and insightful..
Thanks Biosol centre...
Thanks you.
a very informative videos and very clear thank you so much for such kind of platform .... i would request you to please make some videos on docking on MOE please
How to perform HB analysis in Desmond? there are 2 atom subsets that i have to choose. I have tried to create a set for atom subset 1, one amino acid, and for atom subset 2: other amino acids. However, it failed to work. Thank you!
please provide me a link to download the program and whats required process and Ram for laptop to perform molecular dynamics
Is it possible to calculate free energy binding?
How to extract frames and make snapshots out of trajectories: MDS analysis using Desmond
Could you record a video showing how to calculate FEB on the Desmond?
Do you have any dedicated hands on tutorial course to learn Molecular Simulation & Dynamics?? If so please let me know.
Sir plz guide about selection of local host as the software says to activate GPU before running simulation. kindly tell the process to solve this problem
Thank you 🙏
Hi Sir, Whenever i started any job in protein preparation step, it is not updated or incorporated in workspace. so because of that i am not able to perform simulation. Please help me to resolve the issue
Dear Sir or Madam, I am trying to follow your instruction. However, I can not start the job because I can not select a GPU host. The error is cannot start job with dummy GPU host set. Please set a valid CPU or GPU host". Could you please help me with this issue? Many thanks.
Did the issue resolved?
@@saivenkat.d8494 Dear Sir or Madam, I still got stuck in this step. I don't know how to figure it out? I hope you can help me. Thanks.
@@DrHenryNguyen same problem here too
@@saivenkat.d8494 I see. Hope someone can help.
I have the same problem
sir multi sim failure occur in stage ple guide how to rectify the problem
How long will it take to complete 100ns simulation?
Thanks for your enlightening tutorial
but I am facing a problem with desmond
desmond can't find any GPU on my system, but I have an RTX 3060 graphics
what should I do?
Did you got the answer
@@saivenkat.d8494 No 😂
is it free? or Schrodinger required
Best one
Is the software free to download