hello!
I have a small DNA duplex for which there are also noe restraints. I assume
there are 2 or more conformers there, so I want to do a simulation using
LES with restraints. I have a few questions.:
1) Is it possible to model with an explicit solvent? (what will it look
like: does each copy have its own water?)
2) What computing power is required for such calculations? (with an
explicit solvent)
3) when we use LES, we also need to add the -les key for makeDIST_RST: I
have only distance restraints from noesy, do I need to add -les for all
others: makeANG_RST, makeCHIR_RST?
4) how do I figure out how many copies it is better to put? (or do you just
have to try different options and see which one best describes the system?)
Many thanks!
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Received on Fri Jan 31 2025 - 00:30:02 PST
