normal No corresponding bead type can be found for the new molecule

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5 months 2 weeks ago #8172 by Hot
Hi, I'm parameterizing a new molecule, there are some structure no corresponding bead type, such as O=S=O, P=N.
I've run an all-atom simulation of this molecule in acetone. How do I mapping it to CG.

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5 months 2 weeks ago #8174 by riccardo
Hi,
Do you know of experimental free energies of transfer data (e.g., logP) for your molecule or for fragments of the molecule involving those functional groups?
If so, you can compare experimental and computed (see cgmartini.nl/index.php/tutorials-general...titioning-techniques on how to compute free energies of transfer) transfer free energies to validate your bead choice.

I do not have a feeling for how polar the O=S=O group is but a *very* rough guess would be a bead around SP1? I would then compute the free energy of transfer and compare it to available exp data. This paper contain a good collection of exp. data (see the SI: pubs.acs.org/doi/10.1021/ci400112k ).

Regarding P=N: I would recommend to include this group in a larger group of atoms and therefore avoid a 2-atoms-to-1-bead mapping - unless this is really necessary like in small ring-like molecules like benzene. An alternative is to opt for parametrizing the molecule in Martini 3 ( cgmartini.nl/index.php/martini3beta ) ;-)

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5 months 1 week ago #8180 by Hot
Thank you very much for your detailed answer. I have carefully read the information you provided.
In my understanding, does it mean that the beads should be estimated based on polarity first? Then we do the simulation and compute transfer free energy. If the calculated value is similar to the experimental value, that means the beads are a good choice. I wonder if this understanding is correct.
I found that the bead of SO3 is Qa (SQDG in www.sciencedirect.com/science/article/pii/S0005273615000656 ), then SO2 may be Q bead.
The P=N group is contained in a six-membered ring.

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5 months 4 days ago #8183 by riccardo

Hot wrote: Thank you very much for your detailed answer. I have carefully read the information you provided.
In my understanding, does it mean that the beads should be estimated based on polarity first? Then we do the simulation and compute transfer free energy. If the calculated value is similar to the experimental value, that means the beads are a good choice. I wonder if this understanding is correct.

Yes.

Hot wrote: The P=N group is contained in a six-membered ring.


If the structure is 1,2-Azaphosphorine, then you could use a 3 S-bead model like benzene (benzene topology, see here: cgmartini.nl/images/parameters/ITP/martini_v2.0_solvents.itp ) but with a more polar bead for the P=N group. However, if this ring is part of a larger structure (say, something like this: 2-Phenyl-1,2-azaphosphinane 2-oxide), I would recommend to go for 3-atoms-to-1-bead mapping instead of the 2-to-1 mapping you have in molecules like benzene.

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5 months 3 days ago #8184 by Hot
After further study, I think I should take your advice of using a 3 S-bead model like benzene

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