In my opinion - VMD. But it still depends on your needs. Some love YASARA, some love Schroedinger suit (and it's helpfull tutorials....)
Which MD engine you want to use?
I use mainly NAMD, but it can be used with other engines (especially to analyse results).
It's free (for academic use), it has nice online support (tutorials, mailing lists) and has a lot plugins (mostly built in) to do a lot of nice modelling things.
Obviously & once again - all depends on your needs. What do you want to do?
I am interested in the opinion about the available software. What is good, what is bad, what is missing?
If I understand correctly, Desmond is a console application.
Do you probably mean the Maestro?
But VMD is only a visualization program, not a MD package. You can't build models with it.
That's right. I am primarily interested in the models construction.
I know the graphics MD program: MOE, Ascalaph, HyperChem, YASARA.
I like the first two. With YASARA I was not working.
I installed VMD. Indeed, it looks like the trajectories reader only .
I guess VMD is one of the best graphics program to build models, you can get also Hyperchem or Gaussview
If you only need to sketch and display molecules you can use Accelrys Discovery Studio Visualizer http://accelrys.com/products/discovery-studio/visualization-download.php The visualizer is free to download.
If you also need to run MD calculations, then this is perhaps not your best choice since the MD engine is not free
@Mostaganem
How to do it? I do not see the building functions in VMD.
Hi, it is not very clear to me what do you mean! If you wish you create a peptide and be able to visualize it while you are building it. You can probably use xleap which is one of amber tools. You can also use tleap which doesn't have the visual tool but you can always save a pdb and visualize it with VMD.
For organic molecules and drugs, I use mercury which is able to read in Cambridge data base ... and again save it as pdb or ather portables
Under building I mean the ability to make a model from scratch. For example, I inventing a ligand that would bind to DNA. I have to create a 3D model of DNA with the appropriate sequencing, then the model of the ligand. Put it in the DNA. DNA was placed in a box with water. Associate a force field to all this.
Alexey, I would used xleap, as I said it is one of the amber tools and you can import DNA and ligan force field, also the force field for the water. Moreover, you can visualize all the steps.
If you don't have the pdb, then you can start from scratch by writing the sequence of your peptide.
Where do you get the ligand (non-peptide, developed in the mind) and the force field for it?
My favourite tools for molecular building are MOLDEN and GABEDIT. Both free.
Good luck.
Thank all for answers.
However, there is an interesting situation. No one said how to solve the problem: building a ligand out of the head; associate force field; insert it into the biomolecule; perform molecular dynamics. I can suppose that those who design novel ligands stop dealing docking and do not make dynamics. Is that right?
If you are building a single molecule to run in vacuum almost everyone will work fine. However, to prepare a dense system you will need some additional software. I build structures with the Materials Studio Visualizer and Amorphous Cell modules and then use linux homemade scripts to construct DLPoly input files for MD. Preparing an adequate initial structure can be particularly challenging for macromolecular systems. Performing NPT runs to get an adequate density for these systems is sometimes hard, too. In theory, you have many choices of software to perfom MD, but their practical implementation to relative complex systems is nor easy if you want to publish reliable results, not anything coming out from the computer as it is sometimes the case.
I suggest NAB (a module in amberTools package) for Nucleic acid model building.
Nucleic acid builder (nab) is a high-level language that facilitates manipulations of macromolecules and their fragments. nab uses a C-like syntax for variables, expressions and control structures (if, for, while) and has extensions for operating on molecules (new types and a large number of builtins for providing the necessary operations). We expect nab to be useful in model building and coordinate manipulation of proteins and nucleic acids, ranging in size from fairly small systems to the largest systems for which an atomic level of description makes good computational sense. As a programming language, it is not a solution or program in itself, but rather provides an environment that eases many of the bookkeeping tasks involved in writing programs that manipulate three-dimensional structural models.
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