From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Tue Feb 18 2014 - 20:12:14 CST
Do you mean dendrimers that contain coumarin moieties? In that case, if
you don't have a solid plan for generating parameters for the dendrimers,
I feel I would be doing you a disfavor by giving you the coumarin parameters.
On 02/18/2014 04:11 AM, Anna Borlsky wrote:
> Dear Kenno,
> 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.
> Kind regards,
> 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
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