normal create topology file for sophorolipid

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7 years 10 months ago #5592 by Stéfane
create topology file for sophorolipid was created by Stéfane
Dear all,

I would like to construct a MARTINI model of a sophorolipd molecule* (w/o double bond) I have found the parameters for headgroup.and for the alkyl chain. My question is how to model the COOH group at the end of the alkyl chain and the CH3 group in bounded to second alkyl chain carbon (i.e. which bead I choose use)?

*http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/Articleimage/2013/SM/c3sm50160d/c3sm50160d-f1.gif

Thanks

Stéphane

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7 years 9 months ago #5688 by riccardo
Replied by riccardo on topic create topology file for sophorolipid
Hi Stéphane,

Looking at the Martini example in the 2007 Martini paper, I'd modelled a COOH group as SP3 (use of a small particle because of the 3-to-1 mapping). A -CH3 contains one heavy atoms so cannot be mapped to one bead. You should include it in a bigger group, and whether you include it in a group which contains also the oxygen connected to the ring or not really depends on how you place your beads (and will affect the bead choice). If you post some more details about your mapping (i.e., picture with beads and underlying atomistic structure would be ideal) I can be more helpful and recommend you something. Just remember to try to use as much as possible a 4-to-1 mapping.

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