Hello, the only difference will be the Charmm files used during the psf generation and the simulation. These are discussed in nodes 24 and 25 of the NAMD tutorials. The links within these pages to the Mackerell group is where to get the most updated Charmm files and information about which ligands are supported. My videos are outdated with regard to the Charmm files. www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node24.html
Dear Troy thanks for the very informative tutorial. Please let me know how we can apply forced field (amber or any other one) and the addition of Na and Cl into our solvent box through VMD? we will be thankful to you.
I do not know. I remove all ions when I simulate because they tend to cause problems. You can search the namd mailing list to see if there is a solution (www.ks.uiuc.edu/Research/namd/mailing_list/).
Thank you for this awesome videos Dr Troy. I did the same steps as the videos and when I click Run NAMD the status doesn't change to running it gives ready all the time, and three files only are created and the DSD file is not one of them but nothing happens after that. I can't find the problem although I am using a computer workstation.
+Кирилл Щербаков You will need to find the topology files that have descriptions of your lipid-ligand. If it is a common molecule, I am sure the topology exists. You might check here (mackerell.umaryland.edu/charmm_ff.shtml). If it is uncommon, you will need to create this file. I have never needed to create a topology file. There are tutorials for creating them (www.ks.uiuc.edu/Training/Tutorials/science/forcefield-tutorial/forcefield-html/node6.html). Good luck!
Hello Troy, another excellent tutorial. Many thanks. But at 13:31,clicking OK after completing the cell options, i get a message "atomset:frame '-1' invalid;please use a number >=0 or 'first','last',or 'now' while executing. It makes no difference if First Time Step in NAMDgui reads zero or one. Would very much appreciate your comments.
Sorry, I don't. There is nothing at the time 13:31 that I would expect to give an error. The measure minmax could give an error similar to that. atomset is not a VMD command that I am aware of. Have you tried running a vacuum simulation to make sure everything works for your molecule before trying more advanced explicit solvent methods?
+Krishnashish Bose VMD has a CUDA version. I don't know if there are any differences in running the software from non-CUDA versions. VMD software is here (www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD). The site has information regarding VMD and CUDA (www.ks.uiuc.edu/Research/vmd/cuda/).
Sir, thanks for the tutorials.Really helpful! But sorry sir, dumb question, how can I neutralise the systems (addition of Na+ ions). Appreciate your reply. Thank you very much sir!
hi,when I ran the protein -ligand complex simulion with namd2 got angle parameters fatal error for some complexes .How can I overcome.I am new to scripting.So please help me.
Thank you sir uploading the video Kindly provide the Parameter (topology) files necessary for generation of ligand psf as I want to simuland a protein ligand complex simulation.
I do not create topology files. If your ligand has atoms that are not typical, you will need to find the topology file online. The Mackerell Group maintains many Charmm topologies (mackerell.umaryland.edu/charmm_ff.shtml). If they do not have what you need, you may need to create it yourself.
Hi, thanks a lot for your tutorials! When working with phosphoserine I get an error: UNABLE TO FIND BOND PARAMETERS FOR CT2 ON2. Where exactly do I have specify the topology files? In the namd-config they are not allowed with parameters keyword.
Corni Gertling Hi, I'm glad you caught the error. It took me a lot of trial and error before I figured out the topology files necessary for various molecules. I'm still learning.
Hey, thanks for making this tutorial. I encountered an error that I am not able to fix. I followed all the steps as per the video but I'm not able to generate the .dcd file for my simulation. I'm running a 1 ns simulation and when I click on Run NAMD, it shows the status as "Running..." for a second then goes back to saying "Ready". There is no .dcd file in the directory and the output .out file is completely empty with a size of 0 kb. Please respond. Thank you
Have you changed directory in TkConsole so that your simulation directory is where VMD is pointing, e.g., cd ../../../Users/TheRagingTyranitar/NAMD_simulation? What files are in your simulation directory after it stops running?
@@PushpakB541 Two more questions... Have you updated your path variable to tell Windows and VMD where the NAMD executable is located? If you open TkConsole when you try running the simulation, does any output show up there?
@@PushpakB541 Try setting up the simulation and then clicking "Write NAMD config file". Open this file and see what's in it. I think it'll be something.namd. You can paste the contents in a reply here if you want.
These tutorials are very helpful, thank you! When I try to run a NAMD simulation on a protein in a water box, I get an error message that seems to say the water molecules aren't parameterized. I'm using the par_all27_prot_lipid_na.inp included with VMD as the parameter file. What can I do to get around this?
It might be some other setting. Have you set the water to rigid? Here is a NAMD tutorial that discusses water boxes. www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node26.html
@@TroyMessina Sorry, I misspoke - the parametrization issue comes up when I try to generate a .psf file for a solvated .pdb using AutoPSF, or when I enable "Add solvation box" under its Options. Attempting to run a NAMD simulation with the .psf and .pdb files generated by solvating the protein *after* obtaining a .psf from AutoPSF results in an error saying "FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT". Setting the water to rigid does not change any of this.
@@BillNyeTheRussianSpy From what I found on NAMD mailing list it is from solvating and creating psf with tip3p water. You'll need another parameter file. www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2012-2013/3534.html www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2013-2014/1417.html
@@TroyMessina That fixed the parameterization issue, but now trying to run the simulation results in "FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OCL".
It depends on the dcdfreq you set. If you save every timestep (dcdfreq=1, not recommended), you will have 10 ns/ 0.000002 ns = 5 000 000 frames. dcdfreq divides this number by its value, e.g., dcdfreq =500 gives 10 000 frames. Unless you are using an HPC cluster, it's probably best to split a 10 ns simulation into smaller pieces.
Hello, would you please tell me if it is possible to run one simulation and have NAMD automatically spit out one pdb structure at regular intervals until reaching the end of the simulation (where it would then spit out the last pdb structure)? How would this be implemented if it were possible? As an example, I would like to run a protein for a total of 2 nanoseconds and have NAMD crunch out a structure every 0.2 nanoseconds for a total structure ensemble consisting of 10 structures. Would I have to alter the configuration file 'timestep' and 'run' variables or is there some other file where such instructions can be implemented? Thanks again!
Can you give me a quick guide to run protein:ligand simulation using VMD interface to NAMD. I appreciate very much your videos, all 13 clips (molecular modeling in the curriculum). I plan to write up short step by step for myself and our group with printscreen pic in it. Without able to run protein:ligand simulation, my attempts stops here. I have tried to make psf for my ligand, it did not work.I have used open babel to convert my ligand to a pdb structure and that is not accepted by VMD looks like. Will be very grateful to see your steps. thanks a million
Do you have a specific example? Is this a protein structure that you have docked the ligand manually? Or is it a protein:ligand structure you obtained from the pdb as a complete structure?
I want to try run several set of protein and ligand actually. 4l2h is a pdb id for example. It has its ligand. I wanted to analyze the interactions. I tried creating psf after trying to clean up some of the cofactor and unwanted glycerol etc. for the moment. Wanted to keep the ligand part only. I have tried to merge the protein and the ligand. First of all ligand pdb structure is not taken as valid by the vmd. I have used molegro to convert the ligand to pdb as open babel made strange pdb that was not taken by the VMD. Here is my email: sheulizatgmaildotcom. Will u email me I will like to send you the pdb etc. I have recently got permission to use desmond to run protein ligand but feel like know VMD/NAMD almost. Thanks a lot again.
As a practice of the software i ant o send 4l2h complex that has a ligand already. I want to try run several set of protein and ligand actually. 4l2h is a pdb id for example. It has its ligand. I wanted to analyze the interactions. I tried creating psf after trying to clean up some of the cofactor and unwanted glycerol etc. for the moment. Wanted to keep the ligand part only. I have tried to merge the protein and the ligand. First of all ligand pdb structure is not taken as valid by the vmd. I have used molegro to convert the ligand to pdb as open babel made strange pdb that was not taken by the VMD. Here is my email: sheulizatgmaildotcom. Will u email me I will like to send you the pdb etc. I have recently got permission to use desmond to run protein ligand but feel like know VMD/NAMD almost. Thanks a lot again.
Which molecules do you consider the cofactor, unwanted glycerol, and ligand? I only see protein, AR6?, and water. This is a less common pdb file. Every ATOM is duplicated with ANISOU for anisotropic details. You'll probably need to read more about dealing with these in VMD/NAMD if you want to keep them. If not, from VMD you can save a pdb using something like set prot [atomselect top "protein or resname AR6"] $prot writepdb 4L2H_prot.pdb But there is still an issue with some amino acids being labeled things like ASER, BSER, CSER. I'm not sure how to handle that.
This video playlist is very helpful! please guide me on simulation of my protein+ ligand file .while generating.psf file it gives extra topology requirements and opens paratool.Please guide me on simulation of docked file
This is a very broad question. Without knowing many details about your protein and ligand, I cannot offer any advice. If you need topology files, the first place to look is at the Mackerell group (mackerell.umaryland.edu/charmm_ff.shtml), who creates the Charmm topology files. If they have not created what you need, you can search the NAMD forum (www.ks.uiuc.edu/Research/namd/mailing_list/). If they cannot help, you may have to create your own topology. I have never needed to do this, personally. Therefore, I cannot be of assistance.
Hey, its a very helpful video. But while running namd its showing following error error deleting "dock_wb_md.out": permission denied error deleting "dock_wb_md.out": permission denied while executing "error $var " (procedure "::NAMDgui::run" line 69) invoked from within "::NAMDgui::run" invoked from within ".namdgui.go.go invoke" ("uplevel" body line 1) invoked from within "uplevel #0 [list $w invoke]" (procedure "tk::ButtonUp" line 24) invoked from within "tk::ButtonUp .namdgui.go.go" (command bound to event)
I'll need more information. What operating system are you using? Have you modified your PATH variable so that your operating system knows the location of NAMD? Do you have write permission to the folder where your simulation is saving files?
Hello Troy i have some problems regarding number of frames. Say i want to run MD simulation for 1ps, I will do that by keep number of steps as 1000 and by keeping the time step as 1 fs (in basic parameters) . Now the problem is that if i do this number of frames which i got is 40 which implies for each frame has 25 fs. But what i want is that each frame should have 10 fs. or in other words for 1 ps of MD simulation i want 100 frames . Is there a way to increase the number of frames??
Ksai, there is a setting in the NAMD Graphical User Interface. Go to Edit -> Other simulation parameters. In that menu change the DCD/XST output frequency to 10 steps.
Hello, 1st of all, your videos are great-THANK YOU! Second of all, I would like to watch your videos in this series in sequential order-how do I do this? I see your videos, but I can't make out which one is the first in this series, and which video follows and so on. Thanks.
I've mutated and solvated a protein and am now trying to run a minimization and MD simulation on it, but it stops after the minimization. I looked into it further, and it seems the simulation is crashing because "Atoms moving too fast; simulation has become unstable." Any tips?
@@TroyMessina Also, for a different simulation I'm doing involving a point-mutated Trp zipper (using PDB 1LE0 as wild type) in a water sphere, I'm getting "FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HB2 CT1 NH3 (ATOMS 1 5 8)" when I try to run it. I'm using toppar_water_ions_namd.str and all five of the "par_all36" files included with VMD 1.9.3 as parameter files for NAMD.
@@BillNyeTheRussianSpy I don't know all of your simulation parameters. Another possibility that comes to mind is rigid bond settings. There are quite a few posts on the NAMD email list if you search google for "Atoms moving too fast; simulation has become unstable."
@@TroyMessina Never mind, I figured it out - NAMD was failing to minimize the structure after I ran Mutator on it. I worked around this with a different program. Thanks anyway.
Hi, I wondered if you could give me any advice on a problem I'm having with NAMD/VMS? I've just started using both programs (always used pymol before getting interested in simulating dynamics). I run Windows 10 and have downloaded the WIN32 NAMD and the latest VMD that works on my system. The main problem I'm having is that I cannot change the directory that things are being saved to, etc. I've tried changing directory in my commands prompt box, and also through Tk consol. Doing the commands in my command consol does nothing to where things are being saved or directed, and doing it in the Tk consol it gives me: Main console display active (Tcl8.5.6 / Tk8.5.6) (VMD) 1 % cd >Main< (User) 2 % dir .: .VirtualBox .android .idlerc .multiseqdb .multiseqrc .oracle_jre_usage 1UBQ_autopsf.log 1UBQ_autopsf.pdb 1UBQ_autopsf.psf 3D Objects Contacts Desktop Documents Downloads Favorites Intel Links Music OneDrive Pictures Saved Games Searches Tracing Videos VirtualBox VMs autoimd bang my_namd_output_file.out namd tutorial vmd.rc >Main< (User) 3 % cd namd tutorial wrong # args: should be "cd ?dirName?" >Main< (User) 4 % cd desktop >Main< (Desktop) 5 % dir .: Chrome App Launcher.lnk New folder Pract Pro VMD 1.9.2.lnk Zip Files assemble-bc1-notext-stamp.tiff >Main< (Desktop) 6 % dir .: Chrome App Launcher.lnk New folder Pract Pro VMD 1.9.2.lnk Zip Files assemble-bc1-notext-stamp.tiff namd tutorial >Main< (Desktop) 7 % cd namd tutorial wrong # args: should be "cd ?dirName?" >Main< (Desktop) 8 % The "namd tutorial" directory is a file that contains files for the NAMD online tutorial that you can do. I've also followed your tutorials as much as I can, but without the files saving and being somewhere that I can find it's hopeless. Any advice would be greatly appreciated.
+Axx Crz The Tk Console is where you will want to change directories. The command prompt is not connected to VMD. It looks like your directory name "namd tutorial" has a space in it. You might try removing the space. Alternatively, you can type "cd namd" then hit the Tab key. This will autofill with what Tk Console sees as the directory name. Spaces in folder and file names are generally trouble when it comes to console work.
Hi Troy Messina, all initial steps performed correctly, when i hit Run NAMD, the status shows running, but a error message pops up saying , even tk console shows and the directory shows incomplete .namd file. Im working on windows 10, 64bit, i5CPU, intelHD, RAM 6GB. Is it the system not allowing the program to or its the program itself. Please advice. Thanks..
I have updated the location, it is seen in the environment variable, so the tk console ran correctly showing correct directory. namd2.exe stopped working, 3 md files are created in the folder NAMD, OUT and fixed PDB. OUT file (5kb) ended saying FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HB1. NAMD file (2kb) ended saying # Scripting (for temperature).
It could be several things. 1) You are missing a topology file. 2) Your topology files are out of date. 3) Your protein has an atom that needs to be aliased. You should search the University of Illinois mailing list (www.ks.uiuc.edu/Research/namd/mailing_list/).
Plz guide me how to correct protein structure using extension--modeling--fix chirality, fix cis peptide bonds, and create topology parameter file.....I am struggling....badly......Help me out
I have no idea. I have never needed to make those corrections. It appears there are plugins (www.ks.uiuc.edu/Research/vmd/plugins/chirality/ & www.ks.uiuc.edu/Research/vmd/plugins/cispeptide/) and tutorials (www.ks.uiuc.edu/Training/Tutorials/science/structurecheck/tutorial_structurecheck.pdf) for this.
Thank you sir for the informative video. I followed through your entire video but when i hit run namd.. the status comes off as "running" but only for few seconds and then it shows status: ready. Neither .dcd nor .xst files are generated. Your help will be most appreciated Sir...
Does your attempt to run the simulation produce a .log file or some other output file that contains the particular error?The error will be at the end of the .log file. Please paste the error in a reply to this comment.
@@TroyMessina Thank you for the video. I follow the tutorial and I happen to have the same problem. My error that is indicated at the end of the .log file is FATAL ERROR: UNABLE TO FIND "PSF" STRING IN PSF FILE solvate.psf What should I do next? Thank you in advance
@@yagmurkafali2998 I have never encountered that error, and I don't understand from your question what the purpose of the file solvate.psf is. Are you certain your configuration is properly pointing to the location of solvate.psf?
@@yagmurkafali2998 Setting up the NAMD GUI described in this video is the configuration. It is important that the files you are using are in the location specified in the NAMD GUI. I do not use files titled "solvate.psf" in this video. Therefore, I do not know what this file is or how it is being used. I will need more information.
@@TroyMessina when i clicked on run namd, it run for 1 sec shows status ready, in the wrking directory, 3 bew files getting generated except the dcd file.
Rohan Narkhede yes, but you may need special topology files depending on what the ligand is. Read the .out or .log file to see what errors you are getting.
I have also generated topology file for ligand from LigParGen. In .out file, it shows DCD file name: output.dcd and at last it shows FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HB1 Please help sir
hello, your vedios are really helpful. thank you. but, even after performing almost same steps my NAMD has been running from around 10 hours now. does it take this much time? my protein has 44836 atoms and not getting about the no. of frames, as mine is coming zero only. please help. thanks.
Hi Jhumi, It will depend on the number of steps, the step size, and some other factors. Ten hours may be reasonable if you are trying to simulate 10 ns with 1 or 2 fs timesteps. Can you provide more details? You can always open the .log file to see how far the simulation has progressed.
thanks for your reply. minimaization steps -1000 and molecular dynamics steps -100000, multiple time stepping-time step (fs) has set up to 25fs and first time set : 25 and the simulation has progressed till 13618 atoms only. please advise.
You might try running a minimization only. If your timestep is 25 fs, that is probably too long. Try 1 or 2 fs. The number of timesteps per output can be 50 or 100.
hey!! Troy Messina first of all many thanks to you for this video its been of great use to me but i just have one problem that after doing everthing according to what you told in the video when i click on run namd it shows "namd2.exe has stopped working" can you help me with this problem!! i have editted the windows path variable for namd also but still getting this error please help me!!! Thanks..!!
Try to open namd2.exe file . It will show some error message saying some file is missing. Note that missing file and google it. You will find a way to fix that error. After the error got fixed i hope that u will be able to run namd from vmd interface.
Ksai is correct. Usually if your path variable is set, it will be a directory hierarchy problem. For example, your pdb, psf, and topology files are not correctly indicated.
also could someone please help me with another thing that how to simulate any protein through NAMD but without using VMD....plz i really need it as it is urgent and my thesis depends on all this...
+devadrita dey sarkar xsc, dcd, and log files are created during the simulation by namd. If they aren't in your simulation directory, your simulation did not run. You may want to go through the tutorials on the namd/vmd site to learn how to use the software (www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-win-html/index.html). Command line use of namd is MUCH more complex than running through VMD. If you are truly trying to understand something new about your protein, these simulations and analysis will take approximately 6 months to 2 years to get meaningful results. This is not a process that can be rushed.
Thank you for uploading these tutorials! Helpful and easy to follow.
Thank you for video. Can you shared ligand-protein MD using NAMD?
Hello, the only difference will be the Charmm files used during the psf generation and the simulation. These are discussed in nodes 24 and 25 of the NAMD tutorials. The links within these pages to the Mackerell group is where to get the most updated Charmm files and information about which ligands are supported. My videos are outdated with regard to the Charmm files. www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node24.html
Dear Troy thanks for the very informative tutorial. Please let me know how we can apply forced field (amber or any other one) and the addition of Na and Cl into our solvent box through VMD? we will be thankful to you.
I do not know. I remove all ions when I simulate because they tend to cause problems. You can search the namd mailing list to see if there is a solution (www.ks.uiuc.edu/Research/namd/mailing_list/).
Thank you for this awesome videos Dr Troy. I did the same steps as the videos and when I click Run NAMD the status doesn't change to running it gives ready all the time, and three files only are created and the DSD file is not one of them but nothing happens after that. I can't find the problem although I am using a computer workstation.
Hello and thanks for a video, first of all.
But could you help: wthat i got to do to run a simulation of a protein with a lipid-ligand?
+Кирилл Щербаков You will need to find the topology files that have descriptions of your lipid-ligand. If it is a common molecule, I am sure the topology exists. You might check here (mackerell.umaryland.edu/charmm_ff.shtml). If it is uncommon, you will need to create this file. I have never needed to create a topology file. There are tutorials for creating them (www.ks.uiuc.edu/Training/Tutorials/science/forcefield-tutorial/forcefield-html/node6.html).
Good luck!
Hello Troy, another excellent tutorial. Many thanks. But at 13:31,clicking OK after completing the cell options, i get a message "atomset:frame '-1' invalid;please use a number >=0 or 'first','last',or 'now' while executing. It makes no difference if First Time Step in NAMDgui reads zero or one. Would very much appreciate your comments.
Not sure. Do you have your molecule (psf and pdb) loaded into VMD?
Yes Troy...did it exactly as per your video... Baffled why it thinks there is a frame numbered -1?
Hi Troy...sorry to bother. Do you have any more thoughts about this?
Hi Troy...sorry to bother. Do you have any more thoughts about this
Sorry, I don't. There is nothing at the time 13:31 that I would expect to give an error. The measure minmax could give an error similar to that. atomset is not a VMD command that I am aware of.
Have you tried running a vacuum simulation to make sure everything works for your molecule before trying more advanced explicit solvent methods?
Thanks for the video. How can I build alpha quartz via inorganic builder?
I don't know.
Thanks a lot for the great tutorial video.
If I want to use NVIDIA GPU (either Open CL or CUDA), what do I have to do?
+Krishnashish Bose VMD has a CUDA version. I don't know if there are any differences in running the software from non-CUDA versions. VMD software is here (www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD). The site has information regarding VMD and CUDA (www.ks.uiuc.edu/Research/vmd/cuda/).
Sir, thanks for the tutorials.Really helpful! But sorry sir, dumb question, how can I neutralise the systems (addition of Na+ ions). Appreciate your reply. Thank you very much sir!
www.ks.uiuc.edu/Research/vmd/plugins/autoionize/
really useful. Thank you so much.
Glad it helped.
i dont have the log file either?
hi,when I ran the protein -ligand complex simulion with namd2 got angle parameters fatal error for some complexes .How can I overcome.I am new to scripting.So please help me.
I do not know without specific error information. It may be that your ligand and/or protein are not properly defined in the pdb or psf files.
Thank you sir uploading the video
Kindly provide the Parameter (topology) files necessary for generation of ligand psf as I want to simuland a protein ligand
complex simulation.
I do not create topology files. If your ligand has atoms that are not typical, you will need to find the topology file online. The Mackerell Group maintains many Charmm topologies (mackerell.umaryland.edu/charmm_ff.shtml). If they do not have what you need, you may need to create it yourself.
Hi, thanks a lot for your tutorials! When working with phosphoserine I get an error: UNABLE TO FIND BOND PARAMETERS FOR CT2 ON2. Where exactly do I have specify the topology files? In the namd-config they are not allowed with parameters keyword.
Hula Cornula ok i found the error. one should not add the .rtf but only the .str file to the parameters.
Corni Gertling Hi, I'm glad you caught the error. It took me a lot of trial and error before I figured out the topology files necessary for various molecules. I'm still learning.
Hey, thanks for making this tutorial. I encountered an error that I am not able to fix.
I followed all the steps as per the video but I'm not able to generate the .dcd file for my simulation. I'm running a 1 ns simulation and when I click on Run NAMD, it shows the status as "Running..." for a second then goes back to saying "Ready". There is no .dcd file in the directory and the output .out file is completely empty with a size of 0 kb.
Please respond. Thank you
Have you changed directory in TkConsole so that your simulation directory is where VMD is pointing, e.g., cd ../../../Users/TheRagingTyranitar/NAMD_simulation? What files are in your simulation directory after it stops running?
@@TroyMessina yes I've changed the directory. The files after simulation are 1 namd file and 1 out file. Both empty.
@@PushpakB541 Two more questions... Have you updated your path variable to tell Windows and VMD where the NAMD executable is located? If you open TkConsole when you try running the simulation, does any output show up there?
@@TroyMessina Yeah path variable is updated. TkConsole shows "NAMD is running..." and that's all. Nothing else.
@@PushpakB541 Try setting up the simulation and then clicking "Write NAMD config file". Open this file and see what's in it. I think it'll be something.namd. You can paste the contents in a reply here if you want.
These tutorials are very helpful, thank you!
When I try to run a NAMD simulation on a protein in a water box, I get an error message that seems to say the water molecules aren't parameterized. I'm using the par_all27_prot_lipid_na.inp included with VMD as the parameter file. What can I do to get around this?
It might be some other setting. Have you set the water to rigid? Here is a NAMD tutorial that discusses water boxes. www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node26.html
@@TroyMessina Sorry, I misspoke - the parametrization issue comes up when I try to generate a .psf file for a solvated .pdb using AutoPSF, or when I enable "Add solvation box" under its Options. Attempting to run a NAMD simulation with the .psf and .pdb files generated by solvating the protein *after* obtaining a .psf from AutoPSF results in an error saying "FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT". Setting the water to rigid does not change any of this.
@@BillNyeTheRussianSpy From what I found on NAMD mailing list it is from solvating and creating psf with tip3p water. You'll need another parameter file. www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2012-2013/3534.html
www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2013-2014/1417.html
@@TroyMessina That fixed the parameterization issue, but now trying to run the simulation results in "FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OCL".
how do i calculate number of frames ? i want to run simulation for 10ns with time step 2fs ...i want to know how many frames i get?
It depends on the dcdfreq you set. If you save every timestep (dcdfreq=1, not recommended), you will have 10 ns/ 0.000002 ns = 5 000 000 frames. dcdfreq divides this number by its value, e.g., dcdfreq =500 gives 10 000 frames. Unless you are using an HPC cluster, it's probably best to split a 10 ns simulation into smaller pieces.
Hello, would you please tell me if it is possible to run one simulation and have NAMD automatically spit out one pdb structure at regular intervals until reaching the end of the simulation (where it would then spit out the last pdb structure)? How would this be implemented if it were possible?
As an example, I would like to run a protein for a total of 2 nanoseconds and have NAMD crunch out a structure every 0.2 nanoseconds for a total structure ensemble consisting of 10 structures. Would I have to alter the configuration file 'timestep' and 'run' variables or is there some other file where such instructions can be implemented? Thanks again!
Can you give me a quick guide to run protein:ligand simulation using VMD interface to NAMD. I appreciate very much your videos, all 13 clips (molecular modeling in the curriculum). I plan to write up short step by step for myself and our group with printscreen pic in it. Without able to run protein:ligand simulation, my attempts stops here. I have tried to make psf for my ligand, it did not work.I have used open babel to convert my ligand to a pdb structure and that is not accepted by VMD looks like. Will be very grateful to see your steps. thanks a million
Do you have a specific example? Is this a protein structure that you have docked the ligand manually? Or is it a protein:ligand structure you obtained from the pdb as a complete structure?
I want to try run several set of protein and ligand actually. 4l2h is a pdb id for example. It has its ligand. I wanted to analyze the interactions. I tried creating psf after trying to clean up some of the cofactor and unwanted glycerol etc. for the moment. Wanted to keep the ligand part only. I have tried to merge the protein and the ligand. First of all ligand pdb structure is not taken as valid by the vmd. I have used molegro to convert the ligand to pdb as open babel made strange pdb that was not taken by the VMD. Here is my email: sheulizatgmaildotcom. Will u email me I will like to send you the pdb etc. I have recently got permission to use desmond to run protein ligand but feel like know VMD/NAMD almost. Thanks a lot again.
As a practice of the software i ant o send 4l2h complex that has a ligand already.
I want to try run several set of protein and ligand actually. 4l2h is a pdb id for example. It has its ligand. I wanted to analyze the interactions. I tried creating psf after trying to clean up some of the cofactor and unwanted glycerol etc. for the moment. Wanted to keep the ligand part only. I have tried to merge the protein and the ligand. First of all ligand pdb structure is not taken as valid by the vmd. I have used molegro to convert the ligand to pdb as open babel made strange pdb that was not taken by the VMD. Here is my email: sheulizatgmaildotcom. Will u email me I will like to send you the pdb etc. I have recently got permission to use desmond to run protein ligand but feel like know VMD/NAMD almost. Thanks a lot again.
Which molecules do you consider the cofactor, unwanted glycerol, and ligand? I only see protein, AR6?, and water. This is a less common pdb file. Every ATOM is duplicated with ANISOU for anisotropic details. You'll probably need to read more about dealing with these in VMD/NAMD if you want to keep them. If not, from VMD you can save a pdb using something like
set prot [atomselect top "protein or resname AR6"]
$prot writepdb 4L2H_prot.pdb
But there is still an issue with some amino acids being labeled things like ASER, BSER, CSER. I'm not sure how to handle that.
Thank you so much again, I had been waiting to see your reply. I am going to try right now. Thanks for your volunteer generous work and help.
This video playlist is very helpful! please guide me on simulation of my protein+ ligand file .while generating.psf file it gives extra topology requirements and opens paratool.Please guide me on simulation of docked file
This is a very broad question. Without knowing many details about your protein and ligand, I cannot offer any advice. If you need topology files, the first place to look is at the Mackerell group (mackerell.umaryland.edu/charmm_ff.shtml), who creates the Charmm topology files. If they have not created what you need, you can search the NAMD forum (www.ks.uiuc.edu/Research/namd/mailing_list/). If they cannot help, you may have to create your own topology. I have never needed to do this, personally. Therefore, I cannot be of assistance.
Hey, its a very helpful video. But while running namd its showing following error
error deleting "dock_wb_md.out": permission denied
error deleting "dock_wb_md.out": permission denied
while executing
"error $var "
(procedure "::NAMDgui::run" line 69)
invoked from within
"::NAMDgui::run"
invoked from within
".namdgui.go.go invoke"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list $w invoke]"
(procedure "tk::ButtonUp" line 24)
invoked from within
"tk::ButtonUp .namdgui.go.go"
(command bound to event)
I'll need more information. What operating system are you using? Have you modified your PATH variable so that your operating system knows the location of NAMD? Do you have write permission to the folder where your simulation is saving files?
Troy Messina, I'm using Windows 10, I've modified path variable & also have write permission to folder (I've rechecked them)
Hello Troy i have some problems regarding number of frames. Say i want to run MD simulation for 1ps, I will do that by keep number of steps as 1000 and by keeping the time step as 1 fs (in basic parameters) . Now the problem is that if i do this number of frames which i got is 40 which implies for each frame has 25 fs. But what i want is that each frame should have 10 fs. or in other words for 1 ps of MD simulation i want 100 frames . Is there a way to increase the number of frames??
Ksai, there is a setting in the NAMD Graphical User Interface. Go to Edit -> Other simulation parameters. In that menu change the DCD/XST output frequency to 10 steps.
where can i get the xsc file? coz i have run my simulation yet my dcd file has not been formed
Hello, 1st of all, your videos are great-THANK YOU! Second of all, I would like to watch your videos in this series in sequential order-how do I do this? I see your videos, but I can't make out which one is the first in this series, and which video follows and so on. Thanks.
Hi Oscar,
Thanks for the compliment. Here is the link to the playlist.
th-cam.com/play/PLNDQZCI_j92SQ_ipS8ZNxXswFeOsREX4e.html
Troy
Thank you very much! I'll check them out.
I've mutated and solvated a protein and am now trying to run a minimization and MD simulation on it, but it stops after the minimization. I looked into it further, and it seems the simulation is crashing because "Atoms moving too fast; simulation has become unstable." Any tips?
Could be timestep is too big. Could be temperature is too high.
@@TroyMessina The temperature has to be 298 K for what I'm doing, and setting the timestep to 0.5 fs didn't help.
@@TroyMessina Also, for a different simulation I'm doing involving a point-mutated Trp zipper (using PDB 1LE0 as wild type) in a water sphere, I'm getting "FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HB2 CT1 NH3 (ATOMS 1 5 8)" when I try to run it. I'm using toppar_water_ions_namd.str and all five of the "par_all36" files included with VMD 1.9.3 as parameter files for NAMD.
@@BillNyeTheRussianSpy I don't know all of your simulation parameters. Another possibility that comes to mind is rigid bond settings. There are quite a few posts on the NAMD email list if you search google for "Atoms moving too fast; simulation has become unstable."
@@TroyMessina Never mind, I figured it out - NAMD was failing to minimize the structure after I ran Mutator on it. I worked around this with a different program. Thanks anyway.
Hi, I wondered if you could give me any advice on a problem I'm having with NAMD/VMS? I've just started using both programs (always used pymol before getting interested in simulating dynamics). I run Windows 10 and have downloaded the WIN32 NAMD and the latest VMD that works on my system. The main problem I'm having is that I cannot change the directory that things are being saved to, etc. I've tried changing directory in my commands prompt box, and also through Tk consol. Doing the commands in my command consol does nothing to where things are being saved or directed, and doing it in the Tk consol it gives me:
Main console display active (Tcl8.5.6 / Tk8.5.6)
(VMD) 1 % cd
>Main< (User) 2 % dir
.:
.VirtualBox .android .idlerc
.multiseqdb .multiseqrc .oracle_jre_usage
1UBQ_autopsf.log 1UBQ_autopsf.pdb 1UBQ_autopsf.psf
3D Objects Contacts Desktop
Documents Downloads Favorites
Intel Links Music
OneDrive Pictures Saved Games
Searches Tracing Videos
VirtualBox VMs autoimd bang
my_namd_output_file.out namd tutorial vmd.rc
>Main< (User) 3 % cd namd tutorial
wrong # args: should be "cd ?dirName?"
>Main< (User) 4 % cd desktop
>Main< (Desktop) 5 % dir
.:
Chrome App Launcher.lnk New folder
Pract Pro VMD 1.9.2.lnk
Zip Files assemble-bc1-notext-stamp.tiff
>Main< (Desktop) 6 % dir
.:
Chrome App Launcher.lnk New folder
Pract Pro VMD 1.9.2.lnk
Zip Files assemble-bc1-notext-stamp.tiff
namd tutorial
>Main< (Desktop) 7 % cd namd tutorial
wrong # args: should be "cd ?dirName?"
>Main< (Desktop) 8 %
The "namd tutorial" directory is a file that contains files for the NAMD online tutorial that you can do. I've also followed your tutorials as much as I can, but without the files saving and being somewhere that I can find it's hopeless.
Any advice would be greatly appreciated.
+Axx Crz The Tk Console is where you will want to change directories. The command prompt is not connected to VMD. It looks like your directory name "namd tutorial" has a space in it. You might try removing the space. Alternatively, you can type "cd namd" then hit the Tab key. This will autofill with what Tk Console sees as the directory name. Spaces in folder and file names are generally trouble when it comes to console work.
Troy Messina Awesome, thanks for the quick reply!
Just an update, this has fixed my problem! Can't think you enough as this was driving mad.
+Axx Crz Glad to hear it worked. Happy simulating!
Hi Troy Messina, all initial steps performed correctly, when i hit Run NAMD, the status shows running, but a error message pops up saying , even tk console shows and the directory shows incomplete .namd file.
Im working on windows 10, 64bit, i5CPU, intelHD, RAM 6GB. Is it the system not allowing the program to or its the program itself. Please advice. Thanks..
I would need to know more about the error. Either in tk console or the log file. Did you update your Windows path with the location of namd?
I have updated the location, it is seen in the environment variable, so the tk console ran correctly showing correct directory. namd2.exe stopped working, 3 md files are created in the folder NAMD, OUT and fixed PDB. OUT file (5kb) ended saying FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HB1. NAMD file (2kb) ended saying # Scripting (for temperature).
It could be several things. 1) You are missing a topology file. 2) Your topology files are out of date. 3) Your protein has an atom that needs to be aliased. You should search the University of Illinois mailing list (www.ks.uiuc.edu/Research/namd/mailing_list/).
Plz guide me how to correct protein structure using extension--modeling--fix chirality, fix cis peptide bonds, and create topology parameter file.....I am struggling....badly......Help me out
I have no idea. I have never needed to make those corrections. It appears there are plugins (www.ks.uiuc.edu/Research/vmd/plugins/chirality/ & www.ks.uiuc.edu/Research/vmd/plugins/cispeptide/) and tutorials (www.ks.uiuc.edu/Training/Tutorials/science/structurecheck/tutorial_structurecheck.pdf) for this.
Thank you sir for the informative video. I followed through your entire video but when i hit run namd.. the status comes off as "running" but only for few seconds and then it shows status: ready. Neither .dcd nor .xst files are generated. Your help will be most appreciated Sir...
Does your attempt to run the simulation produce a .log file or some other output file that contains the particular error?The error will be at the end of the .log file. Please paste the error in a reply to this comment.
@@TroyMessina Thank you for the video. I follow the tutorial and I happen to have the same problem. My error that is indicated at the end of the .log file is FATAL ERROR: UNABLE TO FIND "PSF" STRING IN PSF FILE solvate.psf
What should I do next? Thank you in advance
@@yagmurkafali2998 I have never encountered that error, and I don't understand from your question what the purpose of the file solvate.psf is. Are you certain your configuration is properly pointing to the location of solvate.psf?
@@TroyMessinaThank you for responding. I am afraid I don't understand what you mean by configuration pointing to the location of my psf file.
@@yagmurkafali2998 Setting up the NAMD GUI described in this video is the configuration. It is important that the files you are using are in the location specified in the NAMD GUI. I do not use files titled "solvate.psf" in this video. Therefore, I do not know what this file is or how it is being used. I will need more information.
hi sir my NAMD on giving the run NAMD command stops running showing error... is there a way that i can run NAMD through command promt
It is difficult to say without knowing the specific error you get. It may be this. th-cam.com/video/I0UfLk8d1SQ/w-d-xo.html
Hi, i cannot getting dcd file please reply
I need much more information.
@@TroyMessina when i clicked on run namd, it run for 1 sec shows status ready, in the wrking directory, 3 bew files getting generated except the dcd file.
Can i follow this procedure to simulate ligand-protein complex
Rohan Narkhede yes, but you may need special topology files depending on what the ligand is. Read the .out or .log file to see what errors you are getting.
I have also generated topology file for ligand from LigParGen. In .out file, it shows DCD file name: output.dcd and at last it shows FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HB1
Please help sir
hello, your vedios are really helpful. thank you.
but, even after performing almost same steps my NAMD has been running from around 10 hours now. does it take this much time? my protein has 44836 atoms and not getting about the no. of frames, as mine is coming zero only. please help. thanks.
Hi Jhumi,
It will depend on the number of steps, the step size, and some other factors. Ten hours may be reasonable if you are trying to simulate 10 ns with 1 or 2 fs timesteps. Can you provide more details? You can always open the .log file to see how far the simulation has progressed.
thanks for your reply. minimaization steps -1000 and molecular dynamics steps -100000, multiple time stepping-time step (fs) has set up to 25fs and first time set : 25 and the simulation has progressed till 13618 atoms only. please advise.
You might try running a minimization only. If your timestep is 25 fs, that is probably too long. Try 1 or 2 fs. The number of timesteps per output can be 50 or 100.
Hi
How can I connect to NAMD2 to run the simulation? thanks
th-cam.com/video/I0UfLk8d1SQ/w-d-xo.html
hey!! Troy Messina first of all many thanks to you for this video its been of great use to me but i just have one problem that after doing everthing according to what you told in the video when i click on run namd it shows "namd2.exe has stopped working" can you help me with this problem!! i have editted the windows path variable for namd also but still getting this error please help me!!!
Thanks..!!
Hi Yash,
I need to know more about the error. If you are using Windows, will you look at the command prompt window and see if there are more details.
I am using windows 10..
it says following in the command prompt
psfplugin) Detected a Charmm PSF file
Info) Using plugin psf for structure file ubq_wb.psf
Info) Analyzing structure ...
Info) Atoms: 2941
Info) Bonds: 2377
Info) Angles: 2827 Dihedrals: 3293 Impropers: 212 Cross-terms: 74
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 646
Info) Waters: 570
Info) Segments: 2
Info) Fragments: 571 Protein: 1 Nucleic: 0
Info) Using plugin pdb for coordinates from file ubq_wb.pdb
Info) Finished with coordinate file ubq_wb.pdb.
Info) Opened coordinate file ubq_wb.pdb for writing.
Info) Finished with coordinate file ubq_wb.pdb.
Info) Opened coordinate file ubq_wb_md_fixed.pdb for writing.
Info) Finished with coordinate file ubq_wb_md_fixed.pdb.
This does not show an error. So, I'm not sure what is causing the crash.
Try to open namd2.exe file . It will show some error message saying some file is missing. Note that missing file and google it. You will find a way to fix that error. After the error got fixed i hope that u will be able to run namd from vmd interface.
Ksai is correct. Usually if your path variable is set, it will be a directory hierarchy problem. For example, your pdb, psf, and topology files are not correctly indicated.
also could someone please help me with another thing that how to simulate any protein through NAMD but without using VMD....plz i really need it as it is urgent and my thesis depends on all this...
+devadrita dey sarkar xsc, dcd, and log files are created during the simulation by namd. If they aren't in your simulation directory, your simulation did not run. You may want to go through the tutorials on the namd/vmd site to learn how to use the software (www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-win-html/index.html). Command line use of namd is MUCH more complex than running through VMD. If you are truly trying to understand something new about your protein, these simulations and analysis will take approximately 6 months to 2 years to get meaningful results. This is not a process that can be rushed.
Ok thanks :-)
Can
Hi