I am interested in doing some in silico mutational analysis on a single loop of a 350-400 amino acids protein and test the mutants for docking (easier part). What would realistically speaking the PC requirements be? I had a quick course in MD but it was mostly docking.
Modeller has been around for a while, with early references to the technique in the mid 90's, and the earliest executable file on the website being from 2002. While the algorithm has certainly been updated, it's not doing substantially more now than it used to - it just does it better. Any reasonably modern computer should be able to handle running the software in a decent timeframe. More important would be the OS - but again, anything reasonably modern (ie: still maintained by the vendor) should be fine. You mention docking - if your computer is capable of docking, I'd tend to expect it to be fine with Modeller.
Note though that Modeller isn't doing MD calculations, it's doing homology modeling, which is much less computationally intensive. If you want to do MD in a reasonable timeframe, that's a whole other question.
@William_P_Katt thank you for the answer. Well that are good news. Could you tell me, by experience, in case of MD calculations what would the requirements be?
MD is a harder question, since there're so many things you might do with it. I can tell you I can run simple MD experiments on a 240 kD protein in water on an ~8 year old linux machine, and the experiment takes about a weekend to run. But MD is, in general, very computationally intensive - if you want to do a lot with it, or use it often, or run really long simulations, a better computer will be of benefit to you. You might also check with your university/department, and see if they have computer clusters you can get time on. You can run a few test experiments, see how long they take, and determine how much data you need, how long you can afford to wait for it, and how much computer you can afford to buy to do the work with.
But if you're really strapped, most of the academic computational chemistry software out there will run on just about anything. Anything bought commercially in the last 5 years or so should be able to run Gromacs or the like just fine - quality of computer will just determine how many hours, or days, you wait for the calculation to finish.
- Badges
- Science topic
- Similar topics
- Chemistry
- Theoretical Chemistry
- Computational Chemistry
- Molecular Dynamics