normal Bond connectivity for Methyl benzoate

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2 years 1 day ago #9416 by shalinijr
Bond connectivity for Methyl benzoate was created by shalinijr
Hi,

Methyl benzoate is modeled as three TC5 beads for the aromatic ring and one N4a bead for the acetate group. In the .itp file for this compound (as shown below), bead 1 (N4a) is bonded to beads 2 and 3 (TC5, TC5) as opposed to just one of them. Could someone help in explaining this?

;;;;;; METHYL-BENZOATE

[moleculetype]
; molname nrexcl
MBZOA 1

[atoms]
; id type resnr residu atom cgnr charge
1 N4a 1 MBZOA O1 1 0
2 TC5 1 MBZOA R2 2 0
3 TC5 1 MBZOA R3 3 0
4 TC5 1 MBZOA R4 4 0

[bonds]
; i j funct length force.c.
1 2 1 0.389 5000 ; cog
1 3 1 0.389 5000 ; cog

Thank you,

Shalini

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2 years 19 hours ago #9419 by vainikka
Replied by vainikka on topic Bond connectivity for Methyl benzoate
Hi,

Methyl benzoate has an elongated square diamond shape (◇) on the CG level. If you went with just a single bond, you'd also need an angle potential to keep the N4a bead oriented correctly. By having two connections, you make a neat triangle with the two TC5 beads, keeping the model simpler.

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2 years 19 hours ago #9420 by riccardo
Replied by riccardo on topic Bond connectivity for Methyl benzoate
Yes! An even better explanation of the one I gave here: github.com/ricalessandri/Martini3-small-molecules/issues/9

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1 year 11 months ago - 1 year 11 months ago #9423 by shalinijr
Replied by shalinijr on topic Bond connectivity for Methyl benzoate
Thank you so much for the explanation and the link. It is clear now.
Last edit: 1 year 11 months ago by shalinijr.

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