the construction of molecular models using the Martini 3 force field #42
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I have some inquiries regarding the construction of molecular models using the Martini 3 force field. Could you kindly provide some assistance or guidance on this matter? I am interested in constructing a thiophene five-membered ring with one of the hydrogen atoms replaced by a fluorine atom. I have noted that the original thiophene ring can be mapped as ((TC5)2-TC6). I would like to replace one of the TC5 beads, but I am unable to find in the mapping table how to replace a ring carbon atom and a fluorine atom with a single bead. Specifically, for the structure −CHa)=C(−F)−CHa)=, what type of bead would be most appropriate for this replacement? I would greatly appreciate your assistance in this matter and thank you very much for helping me |
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Replies: 1 comment 1 reply
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Hi @zhangtrzhangtr , this hasn't been really tested, that's why there's no explicit option for this case in Table 1 of the Martini 3 small molecule paper. I would suggest to substitute the TC5 bead that maps one of the −CHa)=C(-H)−CHa)= in thiophene with a TX4e to map the −CHa)=C(−F)−CHa)= group. This choice is based on the SX4e used in Benzotrifluoride (Table 1 of the Martini 3 small molecule paper) and in general the use of X4e for organofluorides (Supplementary Table 24 of the Martini 3 paper). I hope this helps and feel free to follow up. |
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Thank you for your guidance. I will initially try using the TC6-TC5-TX4e mapping for the structure in my calculations. I appreciate your help greatly. |
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Hi @zhangtrzhangtr , this hasn't been really tested, that's why there's no explicit option for this case in Table 1 of the Martini 3 small molecule paper. I would suggest to substitute the TC5 bead that maps one of the −CHa)=C(-H)−CHa)= in thiophene with a TX4e to map the −CHa)=C(−F)−CHa)= group. This choice is based on the SX4e used in Benzotrifluoride (Table 1 of the Martini 3 small molecule paper) and in general the use of X4e for organofluorides (Supplementary Table 24 of the Martini 3 paper). I hope this helps and feel free to follow up.