Hello fellow
CCL’ers, I
find myself increasingly in need of running some force field calculations (e.g.
OPLS) for organic/biological molecules, and am looking for the best way to get
started. I come from an electronic structure background where making an input
file is pretty straight-forward. Choose atomic coordinates (xyz), basis set,
methodology, and run the calculation. Setting up an input file
for the various molecular mechanics methods however seems more complicated. You
can start with the xyz atomic coordinates, but you also have to worry about
various atom types for the same element, atom connectivity,
etc. Can anyone
suggest some software/website/tutorial that would help in setting up an input
file?
I’m leaning towards using DL_POLY (I have experience with this
code for ‘simpler’ systems) with the OPLS force field, but this
isn’t set in stone. OPLS seems to be widely used for the types of
molecules I’m interested in (organics). Thank you,
N. Aaron Deskins Assistant
Professor Chemical Engineering
Department Worcester Polytechnic
Institute Worcester, MA http://users.wpi.edu/~nadeskins |