From: Anna Borlsky (annanamd_at_gmail.com)
Date: Tue Feb 18 2014 - 03:11:42 CST
Thank you very much for your detailed explanation. The next step will be
construct a dendrimer I will not use a biomolecule. If you can send me the
CHARMM parameter set it would be great.
2014-02-16 4:15 GMT+00:00 Kenno Vanommeslaeghe <kvanomme_at_rx.umaryland.edu>:
> In research, as in many other aspects of life, you often have to think a
> few steps ahead. Suppose you somehow succeed to fix up the topology and
> parameter file xplo2d gave you. Then you have *a* force field for your
> molecule. This might enable you "at the begining only to simulate coumarin
> alone", as you put it. But "at the beginning" implies there's a next step?
> What's the next step? Typically it would be to simulate your molecule
> together with a biomolecule. So you'll need a force field for your
> biomolecule as well. But different force fields cannot be assumed to be
> physically compatible. If you followed a CHARMM methodology for
> parameterizing your small molecule and you choose the AMBER force field for
> your biomolecule (or vice versa), any knowledgeable reviewer will shoot
> down your work. If you followed a parameterization methodology that is not
> associated with any biomolecular force field (for example by using
> parameters from MMFF94), well then you can restart from scratch.
> It's a bit worrisome that your mentor apparently didn't warn you about
> these things.
> For the specific case of coumarin, someone in out lab parameterized it a
> few months ago. It's not officially released yet but I can give it to you--047d7bfea07c1fc93d04f2aaa980--
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