From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Thu Feb 20 2014 - 10:35:55 CST
To clarify, you could generate your dendrimers with the CGenFF program at
paramchem.org , then edit the resulting toppar stream file and replace the
program's guesses for the coumarin moiety with our optimized charges and
parameters. That would be a more or less solid plan. However, given the
questions with which you started this thread, you'll have a lot to learn
before you can reliably perform the aforementioned editing of the toppar
stream file. If you plan to go ahead with this, we could continue the
discussion on CHARMM's "Parameter Set Discussion" forum:
On 02/18/2014 09:12 PM, Kenno Vanommeslaeghe wrote:
> 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
>>> 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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