I am thinking of buying YASARA Structure package to use it for Transmembrane ion channel homology modeling, MD simulations etc. I was wondering if someone can help me with understanding this whole procedure. Does YASARA solvates a protein automatically and embeds it in a membrane of desired components? Then do small MD runs to minimize the structures? By "automatic", I mean to say if I don't have to constantly update the source.
And how much time does it take YASARA to do a standard simulation in single 4 core PC?
Please help me.
Before you spend your money on homology modeling software, are you sure you have the right template (sequence identity > 30%), if I may ask?
Yes, I have the right template, sequence identity~50%, sequence similarity~80%. One of the proteins from the same group have been crystallized recently fortunately. I have used MODELLER for homology modeling, and it gives very satisfying results. But I need to do MD simulations also, to analyze some mutants, and alteration in the structure after docking some specific ligands.
I have never used YASARA Structure Package before. But I have some experience with homology modeling of transmembrane protein. I was using MODELLER for homology modeling, VMD for the system preparation (adding membrane, solvating, etc.), and using NAMD for the MD simulation. And from my experience putting the transmembrane protein inside membrane is not a simple task so I don't think it can be done automatically. Because the nonpolar residue area should be aligned correctly with the membrane (sometimes the protein has to be tilted into some degree), check out this discussion: https://www.researchgate.net/post/Can_I_get_an_example_model_of_protein_in_the_lipid_bilayer_for_comparison.
In the past I was simulating the system (consisted of almost 40,000 atoms), and it took 14 days/ns. But that was about 5 years ago, and I was only allowed to use 1 core (out of 4) of Xeon Processor. I think nowadays processor would be sufficient to run your simulation in less than a week. Well, it depends on how many ns you would need and how large is your whole system.
The alignment is available in a bilayer. I need to solvate first and then need to put inside a membrane. And tell me something, these simulations, how much time would they take if allowed all the 8 processors of an intel i7 machine?
I think it should be the opposite, put the protein inside membrane first then solvate (http://www.ks.uiuc.edu/Training/Tutorials/science/membrane/mem-tutorial.pdf).
I don't know, it depends on how large is your system (the number of all atom after the addition of membrane and the solvation process). Also how many ns you would simulate. You mean 4 cores? i7 comes with Hyperthreading that it allows to use 8 thread for a single processor. My guess is if the whole system is around 100.000 atoms, and you only need to run about 2 ns then perhaps it would be done in around 1 week. In most MD package (like NAMD, Gromacs, etc.) there is a benchmarking feature, which in every certain steps (1000 or 2000 steps) it gonna shows the amount of time needed per ns.
Thanks a lot. But I think a little MD run after solvation and then putting into membrane would be better for my system, and my system is going to be huge, around 100000-120000 atoms. So, it's going to take huge time I guess. I will check the benchmarks. And what if I want to run the simulations on CHARMMing server? I don't have much idea though.
Well, most MD package has constraint/restraint feature. In the MD tutorial above the MD is done in steps. The first one is membrane and protein is constrained, only solvent is able to move freely. The second one is the membrane is allowed to move, and protein allowed to move a little bit, then the last one is every atom allowed to move freely.
The problem with adding the solvent first is it will collide with the membrane atoms when the membrane is added later. Removing the water molecule within certain distance from membrane molecule will cause the water at the membrane-water interface need to be re-equilibrated.
Hi Pritam,
I am using an windows machine. And I am not sure if GROMACS will work properly with cygwin, in that case also, I do not have idea. Can you help me in a little bit details?
Best,
Arijit
Rather than waste precious time trying to get cygwin setup correctly in order to support complex modeling applications like gromacs, you better off getting Ubuntu linux or ubuntu variants installed. With a fresh ubuntu install you are one command line away from installing all the structural biology packages you would need.
Deciding to purchase a license for YASARA-Structure was one of the best decisions I have ever made. I cannot say enough positive things about this molecular modeling package. It is user-friendly yet extremely powerful and fast. You can get some idea of the performance in MD simulations by visiting the YASARA site.
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