normal Modeling Fmoc

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9 months 1 week ago #7148 by Sofi@
Sofi@ created the topic: Modeling Fmoc
Hi everybody!

I would like to modelize an Fluorenylmethyloxycarbonyl chloride (F-moc) at the end of a oligopeptide. Does anyone have any idea if it has been done before or will I have to modelize it from the begining?

Thanks a lot for the help,
Sofia Bariami

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9 months 1 week ago #7151 by riccardo
riccardo replied the topic: Modeling Fmoc
Hi,

I don't know of any model for such a molecule, but please check the literature thoroughly.

Otherwise, see tutorials and Martini papers for how to build and validate a model. Here's how I would map it:

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where all but the OCOCl bead are S-beads. S-beads on the aromatic part would be the same as for benzene, so SC5 beads. However, you should also look for experimental partitioning data (also only for fragments of the molecule, in case you don't find data for the whole molecule) against which validate the bead type choices (see tutorials ).

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9 months 1 week ago #7152 by Pim
Pim replied the topic: Modeling Fmoc
Hi Sofia,

Someone affiliated with our group has done some work on Fmoc peptides recently. I will ask him to share his results. Note: the assembly of Fmoc-peptides remained tricky even with the optimized parameters for Martini 2.2.

PS. Thorough atomistic parametrization: pubs.rsc.org/-/content/articlehtml/2016/cp/c5cp06770g

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9 months 1 week ago #7153 by Sofi@
Sofi@ replied the topic: Modeling Fmoc
Thanks a lot!

Yes, I'm using S beads for sure for the aromatic compound in order to preserve the ring geometry. As for the other part, I hope I'll find something in the literature

:)

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9 months 1 week ago #7154 by Sofi@
Sofi@ replied the topic: Modeling Fmoc
Thank you Pim!

That's very useful :)

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9 months 1 week ago #7157 by Tomasz
Tomasz replied the topic: Modeling Fmoc
Dear Sofia,

As Pim mentioned, I've tried to parametrize Fmoc. Unfortunately, my parametrization is not perfect, and it overestimates hydrophobic interactions (experimental logP=1.4 and mine 3.6), so you will need to work a little bit on that. I have used the topology which Riccardo showed. The tricky part was to keep molecule flat - to do that I had to use two virtual sites and bending restriction potential, which requires usage of Gromacs 5. (parameterization is in a similar manner as in this paper: aip.scitation.org/doi/10.1063/1.4937783 )

Below is the topology. For sure it is not perfect, but I think it is a good starting point. You should play more with nonbonded parameters to better reproduce logP. I used timestep 10fs.

Cheers,
Tomasz


[ moleculetype ]
; Name Exclusions
FDP 1

[ atoms ]
1 P5 1 FDP BB 1 0.0000 72.0
2 SC5 1 FDP SC1 2 0.0000 108.0
3 SC5 1 FDP SC2 3 0.0000 0.0
4 SC5 1 FDP SC3 4 0.0000 108.0
5 SC5 1 FDP SC4 5 0.0000 108.0
6 SC5 1 FDP SC5 6 0.0000 108.0
7 SC5 1 FDP SC6 7 0.0000 0.0

[ bonds ]
1 4 1 0.37000 5000 ; FDP
1 5 1 0.36500 9000 ; FDP

[ constraints ]
2 4 1 0.21000 ; FDP
4 5 1 0.19000 ; FDP
5 6 1 0.21000 ; FDP

[ virtual_sites3 ]
3 2 4 5 3 300 0.21000 ; FDP
7 6 5 4 3 300 0.21000 ; FDP

[ angles ]
2 4 5 10 130 200 ; FDP
4 5 6 10 130 200 ; FDP
2 4 1 10 153 100 ; FDP
6 5 1 10 130 100 ; FDP

[ dihedrals ]
2 4 5 6 2 0 50 ; FDP

[ exclusions ]
1 2 3 4 5 6 7
2 3 4 5 6 7
3 4 5 6 7
4 5 6 7
5 6 7
6 7
7

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9 months 1 week ago #7159 by Sofi@
Sofi@ replied the topic: Modeling Fmoc
Hi Tomasz,

Thanks a lot for the info. Helped a lot!
Yes I'll check the parameters as you indicated.

Have a good day,
Sofia

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