@@TroyMessina I have a complex that has protein and ARN. I want to create a pdb file in which protein and ARN be in a box water but one section of box (in which will be ARN) has more padding than the other section of box (in whic will be protein)
@@juanjocepeda5645 Try solvating twice. I think you can do the ARN solvation with more padding. Then, take that result (pdb and psf), and add the bigger/less padded solvation box around everything. It's possible the order will be the opposite of this.
Hi Troy Messina, thank you for such detailed tutorials. I tried solvating modeled (modeled in swissmodel) protein of 40aas, initial tried with 2.4 default boundary, but it seems the water molecules do not cover the protein entirely, so increased the boundary size to 3, still it does not cover the protein. Can you please suggest if there is any error.
Yes i increased it to 5, still it looks like the protein is shifted to one side of the water box and is not fully covered with water molecules. I wish i could have shared the image to make it more clear!
The solvation box is placed with its center at the center of mass of the protein. This will often make some portion of the protein very close to the surface of the box. If you want it buried deeper, increase the solvation in increments of 2.4. Keep in mind that more solvation molecules increases computation time drastically. There is some evidence that water beyond one or two molecules in distance do not interact with the protein. Unless you plan to analyze the solvent interactions, I recommend keeping the solvation to a minimum.
Hey Troy Messina thanx for the tutorial. I have a doubt. the measure minmax command does not return any coordinates. What is the problem. How should I troubleshoot? Please help
+yowan nerthigan Hi, I'm not sure why. Make sure you have a selection to be measured, e.g., set myselection [atomselect top all]. You should see a response from VMD "atomselect#" in the TkConsole. Then, measure minmax $myselection should return a set of values.
+Troy Messina Thank you so much for the suggestion. I have one more question. I have a protein and a ligand. How do I run a MD with NAMD? I know to do this with a single protein but not with a ligand. Please help
yowan nerthigan It will depend on what the ligand is. If it is something common, there is probably a force field for it already. NAMD uses the Charmm topology files for force fields. You can search for it either through the NAMD site or the Charmm site. If you need to create a new force field, the NAMD tutorials are probably the best place to start. www.ks.uiuc.edu/Training/Tutorials/. Take a look at the user-defined forces section.
+Troy Messina hey I was able to create a psf file for the ligand and the receptor. I have a complex of them both and a respective psf file. But I am unable to run Namd. what should i do??
Hi When I did solvation the water totally covered most of the protein and it wasn't clear enough . How can I change the water density to make my protein appear more clearly?
Water has a density of 1g/mL. I don't recommend you change that. You are able to display your protein without the water showing, In VMD use the Graphical Representations interface to create a representation of protein only. www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node2.html
Simulate with and without water to determine this. You can vary the amount of water (number of water layers extending beyond your protein) if you want. It is pretty well known that water will cause proteins to expand compared to vacuum simulations. ac.els-cdn.com/S0006349594805156/1-s2.0-S0006349594805156-main.pdf?_tid=6677f142-7fb8-4b6d-938b-6f2128c74017&acdnat=1538675827_938b43aa868c7075531f2251e1fbf8f0
+devadrita dey sarkar Hi, I do not understand how you obtained a log file without simulating your protein. If you have a protein + ligand pdb file you can generate the psf file using this tutorial (th-cam.com/video/YGP_GM1bfbg/w-d-xo.html). If you need to create the protein + ligand pdb file, you will need to find other tutorials about docking the ligand. That is not something I do.
Hello, you can add a water sphere using tcl scripting. A script is at the link below. It may need modification for your molecule(s). www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node28.html
hello sir i have one doubt that the log file in your folder is already prepared before the simulation...how do i prepare or get the log file ? coz according to the NAMD tutorial log file generation is done after wards...
I do not know what you mean by "separate". Do you want the protein in a pdb file and the ligand in different pdb file? If you want two different files, follow this video for selecting and saving portions of a structure. th-cam.com/video/55iZL0g7Se0/w-d-xo.html Once you save the two files, you can solvate them separately.
Okey ...but I Guess there is another method To do it by using graphic console ....we write all protein that mean protein and ligand But in this case i want just the protein (enzyme) in a file Ligand in another one without using script please
@@keikoyukimura7279 I don't think you can save a pdb from the Graphic console. It is for visualization only. You should read about the atomselect command in the links at the end of my reply. If you use "all protein", you are being redundant. "all" has already selected the protein and everything else in your pdb file. "all" selects everything. "protein" selects protein or enzyme only. Your ligand has some identifier so that you can select it only, e.g., "resname ATP" for ATP molecule. You will need to figure out what this ligand identifier is (See my video on pdb file structure -- th-cam.com/video/Xq9EHBJ80G8/w-d-xo.html). Boolean logic allows you to make selections based on multiple conditions, but I don't think you want this for the task you are attempting. You will need to use Tk Console to write two pdb files. The first one is protein only. The second one is ligand only. set prot atomselect [top "protein"] $prot writepdb protein.pdb set lig atomselect [top "resname ATP"] $lig writepdb ligand.pdb Here are some relevant links. www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node181.html www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node108.html
Do U know how to solvate in two parts the protein?
I'm not sure what you mean. Can you be more specific?
@@TroyMessina I have a complex that has protein and ARN. I want to create a pdb file in which protein and ARN be in a box water but one section of box (in which will be ARN) has more padding than the other section of box (in whic will be protein)
@@juanjocepeda5645 Try solvating twice. I think you can do the ARN solvation with more padding. Then, take that result (pdb and psf), and add the bigger/less padded solvation box around everything. It's possible the order will be the opposite of this.
Can you please show how to solvate a protein with a non-standard solvent? I want to solvate my protein with my ligand molecules and water. Thanks!
I think you will need to use something like packmol (m3g.iqm.unicamp.br/packmol/examples.shtml).
Hi Troy Messina, thank you for such detailed tutorials.
I tried solvating modeled (modeled in swissmodel) protein of 40aas, initial tried with 2.4 default boundary, but it seems the water molecules do not cover the protein entirely, so increased the boundary size to 3, still it does not cover the protein. Can you please suggest if there is any error.
Hi Appy,
I believe 2.4 corresponds to a monolayer of water at the thinnest covering. To get two layers of water, increase to 4.8 or 5 Angstrom.
Yes i increased it to 5, still it looks like the protein is shifted to one side of the water box and is not fully covered with water molecules. I wish i could have shared the image to make it more clear!
The solvation box is placed with its center at the center of mass of the protein. This will often make some portion of the protein very close to the surface of the box. If you want it buried deeper, increase the solvation in increments of 2.4. Keep in mind that more solvation molecules increases computation time drastically. There is some evidence that water beyond one or two molecules in distance do not interact with the protein. Unless you plan to analyze the solvent interactions, I recommend keeping the solvation to a minimum.
Hey Troy Messina thanx for the tutorial. I have a doubt. the measure minmax command does not return any coordinates. What is the problem. How should I troubleshoot? Please help
+yowan nerthigan Hi, I'm not sure why. Make sure you have a selection to be measured, e.g., set myselection [atomselect top all]. You should see a response from VMD "atomselect#" in the TkConsole. Then, measure minmax $myselection should return a set of values.
+Troy Messina Thank you so much for the suggestion. I have one more question. I have a protein and a ligand. How do I run a MD with NAMD? I know to do this with a single protein but not with a ligand. Please help
yowan nerthigan It will depend on what the ligand is. If it is something common, there is probably a force field for it already. NAMD uses the Charmm topology files for force fields. You can search for it either through the NAMD site or the Charmm site. If you need to create a new force field, the NAMD tutorials are probably the best place to start. www.ks.uiuc.edu/Training/Tutorials/. Take a look at the user-defined forces section.
+Troy Messina hey I was able to create a psf file for the ligand and the receptor. I have a complex of them both and a respective psf file. But I am unable to run Namd. what should i do??
+yowan nerthigan I do not know. There can be many issues that keep it from running. You can diagnose by reading the log file.
Hi
When I did solvation the water totally covered most of the protein and it wasn't clear enough . How can I change the water density to make my protein appear more clearly?
Water has a density of 1g/mL. I don't recommend you change that. You are able to display your protein without the water showing, In VMD use the Graphical Representations interface to create a representation of protein only. www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node2.html
thank u, But i need to do simulation and i wanna know if the amount of water affect the simulation result??
Simulate with and without water to determine this. You can vary the amount of water (number of water layers extending beyond your protein) if you want. It is pretty well known that water will cause proteins to expand compared to vacuum simulations. ac.els-cdn.com/S0006349594805156/1-s2.0-S0006349594805156-main.pdf?_tid=6677f142-7fb8-4b6d-938b-6f2128c74017&acdnat=1538675827_938b43aa868c7075531f2251e1fbf8f0
ok i got my log file but i want to simulate the protein and the ligand together but i have different psf files then how do i simulate them together?
+devadrita dey sarkar Hi, I do not understand how you obtained a log file without simulating your protein. If you have a protein + ligand pdb file you can generate the psf file using this tutorial (th-cam.com/video/YGP_GM1bfbg/w-d-xo.html). If you need to create the protein + ligand pdb file, you will need to find other tutorials about docking the ligand. That is not something I do.
Hi, How did you create the pdb file?
That's in the previous video in the series. th-cam.com/video/YGP_GM1bfbg/w-d-xo.html
Sir, how to draw a water sphere?
Hello, you can add a water sphere using tcl scripting. A script is at the link below. It may need modification for your molecule(s). www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node28.html
hello sir
i have one doubt that the log file in your folder is already prepared before the simulation...how do i prepare or get the log file ?
coz according to the NAMD tutorial log file generation is done after wards...
I love you! Thank you so much!
Awww, thanks!
Can you tell me please how can we separate the protein from the ligand
And solvate it in 2 differents files
I do not know what you mean by "separate". Do you want the protein in a pdb file and the ligand in different pdb file? If you want two different files, follow this video for selecting and saving portions of a structure. th-cam.com/video/55iZL0g7Se0/w-d-xo.html Once you save the two files, you can solvate them separately.
Okey ...but I Guess there is another method To do it by using graphic console ....we write all protein that mean protein and ligand
But in this case i want just the protein (enzyme) in a file
Ligand in another one without using script please
@@keikoyukimura7279 I don't think you can save a pdb from the Graphic console. It is for visualization only. You should read about the atomselect command in the links at the end of my reply. If you use "all protein", you are being redundant. "all" has already selected the protein and everything else in your pdb file. "all" selects everything. "protein" selects protein or enzyme only. Your ligand has some identifier so that you can select it only, e.g., "resname ATP" for ATP molecule. You will need to figure out what this ligand identifier is (See my video on pdb file structure -- th-cam.com/video/Xq9EHBJ80G8/w-d-xo.html). Boolean logic allows you to make selections based on multiple conditions, but I don't think you want this for the task you are attempting. You will need to use Tk Console to write two pdb files. The first one is protein only. The second one is ligand only.
set prot atomselect [top "protein"]
$prot writepdb protein.pdb
set lig atomselect [top "resname ATP"]
$lig writepdb ligand.pdb
Here are some relevant links.
www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node181.html
www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node108.html