Have you checked that the par_all27_prot_lipid.inp file is present in that path? 

It is possible that you have to adjust the path to the parameter file. 

 Thanks Oliver, Let me check

Huh, I've been practicing several of  the VMD and NAMD tutorial files so I think I know a thing or two. You're asking this question concerning Microsoft Windows I presume. For several purposes, I'm quite dissatisfied with Microsoft Windows mainly that the command prompt terminal does not recognize several commands I try to pass through it. I suppose you could write a command in subroutine like format in an external executable folder folder but that's too much work and too much room for error. 

First of all, make sure you are in the right folder (1-2-sphere) which from the tutorial I trust you are. I wanted to see what your problem was so I ran your command in my Microsoft 10 Windows command prompt and it worked so I'm a little puzzled. I suppose you could try running the command in Powershell which is basically an educated command prompt and see if it works. Unfortunately, my Powershell does not recognize the ampersand "&" metacharacter so I tried putting it in quotes and I'm seeing if it works. I think the purpose of that metacharacter is to to tell you if there is any error in running the namd2 process to create the log file as the output of which files with the ".log" extension keep an account of successes and failures.  

Of course, if you don't have the par_all27_prot_lipid.inp file in your common folder one folder back then command process won't work. But, it could also be possible that your terminal or namd2 does not recognize the ".inp" extension file which contains the physics of atom bonding interactions assuming a ball-and-spring model. If the latter is the case then that's why I suggested using powershell, else you could join the Windows Insider build and get access to the Unix-like command terminal which Microsoft Windows has been building, but I think more like re-configuring/translating to work in the Windows operating system environment.   

I prefer to run VMD and NAMD in Scientific Linux which I set to duel boot in the "C:/" of my computer, except going into the Scientific Linux 7.2 operating system involves me going into the boot-processes upon "shift-restart". They run perfectly in Scientific Linux 7.2, though on my duel boot I made the mistake of giving Scientific Linux partition too little space so now I'm running out of space for my program; so that's my problem, but I found a way around it with a new computer since I duel-booted in the first place, instead of overwriting Windows, because I need both operating systems for some purposes, though Scientific Linux is compatible with almost all programs I need. 

If you are interested in Scientific Linux which is a Red-Hat like distro from CERN and Fermi National Acceleratory Laboratory, then you can install it from the ISO File by burning the largest iso file to a CD/DVD: 

iso file: SL-7.2-Everything-Dual-Layer-DVD-x86_64-2016-02-02.iso

Source: http://ftp1.scientificlinux.org/linux/scientific/7x/x86_64/iso/

The standard protocol is to install it from the CD and your computer boots. However, if you don't know what you're doing without your files backed up then you could overwrite Microsoft Windows on your computer with Scientific Linux (SL) as the new operating system and lose all your files. SL is kind of a minimalist operating system, but it's easy to install several applications to make it more professional and fun. I like the "Terminator" application upon "yum install terminator". Terminator is a command terminal which you can break up into several terminals in the same window if you intend to run several calls from the command line.   

Note: The configuration file you've downloaded from the Ubiqutin Tutorial File is very complicated so it might be hard to write for another protein you would like to study besides Ubiquitin. However, you can let vmd write the ".conf" file for you with the necessary physics for your whatever protein you've take the pdb code and made the protein structure file (.psf), and then you load the pdb file ontop of the protein structure file in the VMD graphical user interface (GUI) and proceed making the ".conf" file for your protein/protein-complex using "Extensions > Simulation > NAMD Graphical Interface" in VMD.

Troy Messina discusses the protocol for that in this video which is a part of his "Molecular Modelling in the Curriculum" playlist: 

https://www.youtube.com/watch?v=2hEur0xMbiw&list=PLNDQZCI_j92SQ_ipS8ZNxXswFeOsREX4e&index=12

I hope your trouble-shooting works out.

-Adron 

 Thank you so much Adron Ung for this nice suggestion and advice

Thank you very much for your kind suggestion, now I successfully executed it

Thank you very much, Mustafa Alhaji Isa!

I'm trying to figure out how to use NAMD and VMD myself as I still have a lot to learn, and we are all here to learn. If you do choose to use Scientific Linux 7.2 in some way, I suggest installing NAMD and VMD into the directory "/usr/local/lib" or "/usr/local/lib64". That seems to be the equivalent of putting executables into system32 on Windows, though you can do it. Just copy the files there from your downloads folder there, and then, and then unzip/untar the folder, and the instructions for the installation process are in the README file which you can like at without opening with the command "more".

I don't understand what this guy is saying, but what he's typing is how you install VMD from the command line: https://www.youtube.com/watch?v=5TN_DV3F198

You pretty much do exactly the same thing to install NAMD, as well. The installation process is all command-line based, but there is only seems to take about 5 commands from the terminal to install either program. 

Yay! 

Ok Adron Ung, I will try this one also

So you were able to do it in Powershell? 

Yes

Please  Adron Ung, the Video tutorial you sent me is the simulation of protein only 

Can you send me the Video Tutorial of molecular dynamic simulation of protein-ligand complex

Hello Sir,

I am not an authority on how to do these matters, as I'm learning it myself. I can give you some suggestions though. As it turns out, there are not a lot of video tutorials out there which illustrate calculating the thermodynamics of protein-ligand interaction computationally. Most of the video tutorials are just theory not technique. There are more written tutorials for this endeavor.

I would recommend trying out this these tutorials, under the Free Energy methods section: http://www.ks.uiuc.edu/Training/Tutorials/,

particularly this one on the same page: Protein:ligand Standard Binding Free Energies: A Tutorial for Alchemical and Geometrical Transformations.

The tutorial lets you calculate something really neat being the equilibrium constant of a binding reaction with a free-energy plot. (But, the tutorial assumes that you have prior knowledge of NAMD from working through the NAMD tutorials and several other tutorials.) You are expected to be able to generate the protein structure file (.psf) from the PDB coordinate files ... well, hmm, they provided those, actually, maybe in an update.

But anyway, you can generate a psf from a pdb like Troy Messina illustrates, or via a terminal, or in VMD using the tcl scripting language. Anyway, prior knowlege is assumed in the tutorial, and so not all the commands to run the simulation are actually shown in this tutorial. You are expected to be able to infer those, as well as graphing in a spreadsheet utility like xmgrace from the other tutorials on the page.

I don't know if my eyes weren't meticulous enough because I wasn't able to find any tutorials about how to calculate all three thermodynamic constants such as the entropy and enthalpy of a binding event, Gibbs Free Energy included. But, no tutorials in that regard; however, they have been calculated by some scientists, so here is an excellent research paper which calculates those:

Da Zhan, Yingqian A et al. “Impact of the K24N Mutation on the Transactivation Domain of p53 and Its Binding to MDM2.” Proteins 81.10 (2013): 1738–1747. PMC. Web. 7 Aug. 2016.

Direct link: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160123/

Before you run a simulation, make sure to bring the system up to biological temperature (about 310 Kelvin) with minimization and/or equilibration because X-Ray crystallography of proteins is done at near liquid nitrogen temperatures, so you need to do some work with the pdb file and the psf file before you can really consider the structure you see in VMD to be in a relatively correct biological conformation.  

Anyway, good luck!

-Adron

If you have any problems having your commands rejected in Windows, then I would suggest running the simulations in Linux Mint 18 (https://www.linuxmint.com/download.php) in virtualbox (https://www.virtualbox.org/). You don't have to mess with your hard-drive to do it, but  virtualbox will eat up some of the RAM on your computer while you run another operating system, but you can determine how much RAM it uses while LM is running in virtualbox. I'm just a fan of linux.

This might be helpful, as well:

http://vina.scripps.edu/tutorial.html

Thank you very much Adron Ung

I will try and check all

You are welcome. I'm glad I've learned some useful things in my independent study. If you discover anything interesting in regards to this field of study, feel free to let me know.

Have a nice day now.  

Ok, I will