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ricalessandri / Martini3-small-molecules

Martini 3 small-molecule database
https://doi.org/10.1002/adts.202100391
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On the mapping of the N-DMBI molecule #26

Closed Clare-xiong closed 1 year ago

Clare-xiong commented 1 year ago

Hi. I try to map the N-DMBI, but I always miss one carbon in the benzene like this N-DMBI Could you help me mapping N-DMBI correctly?

ricalessandri commented 1 year ago

@Clare-xiong - I'm sorry, this post slipped through my notifications.

Your mapping is almost correct. That missing carbon in the benzene should be mapped together with the -N(CH3)2 (the S-bead you highlighted in green). At first it may look as a slightly "overmapped" S-bead (4 non-hydrogen atoms); however, because it is fully branched, this is the recommended way to map it - see:

"fully branched fragments should usually use beads of smaller size (the rational being that the central atom of a branched group is buried, that is, it is not exposed to the environment, reducing its influence on the interactions); for example, a neopentane group contains 5 non-hydrogen atoms but, as it is fully branched, you can safely model it as a regular bead."

from section 2 of this tutorial.