Not so quite bioinformatics: Molecular Modelling - A question about spartan (Mar/14/2007 )
I greet you all in my first post, which is a question about the molecular modelling program spartan, and some general questions about molecular modelling.
I have a project that is about chlorophylls, of whose details I guess are irrelevant, but the project involves about 10000 atoms of which %95 of them I want to freeze in spartan.
One question is when I freeze atoms in spartan and then do geometry optimizations from the calculations screen it treats the atoms as unfrozen and moves them around. Yes I check the box that says frozen atoms in the calculations window.
Second question, when I try to just energy minimization, the program can't even start doing anything. Is it due to the fact that spartan is not ideal for such large molecules. Is there any way to optimize spartan for large molecules?
Third question, are there any free force fields for god's sake that I can download in ffml extension?
Fourth question is anyone knowledgeable on BALLview? Can you do advanced selections in that program like selecting a whole chain, hiding it and doing MM calculations only on selected parts of the molecule?
Fifth is there a way of installing Gromacs on windows. I tried the setups in the original software website but I was unable to do so. If there is no way, how can I learn to build unix on my machine d: I am starting to hate windows
And no I am not a chemist I am a full time genetics student d: ( I also try to learn bioinformatics but I am rather at raw computer engineering courses right now, I alas dont have any knowledge on bioinformatics).
I have not familiar with Spartan or BALLview but if you want to perform MM calculations on Biomolecules you can use GROMACS or other molecular dynamics simulation packages such as CHARMM or AMBER. It will be possible to perform the calculations only on selected parts of your system too. You should refer to the related user manual to learn how to do that. Moreover, almost all available force fields for bimolecular simulations can be used free of charge. You may probably need to pay for the simulation programs.
Although some of the MD simulation packages could be installed on Windows but installation on UNIX is usually easier. You can obtain a free of charge version of UNIX (like fedora core) on the net. For installation... After completing the download process and writing the images of the downloaded files onto CDs, insert the first CD into the computer and reboot the system. Choose the graphical mode and go on with the installation process. Select the custom configurations if you are not familiar with UNIX. You should be careful while UNIX is partitioning the hard disk and prevent it from formatting the other drives, otherwise you will lost all of the information or the previous O.S. (Windows) on that drive.