normal bead change in martini2 and martini2

  • FJSP22
  • FJSP22's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
5 months 2 weeks ago #9412 by FJSP22
bead change in martini2 and martini2 was created by FJSP22
Hi everyone!
I have to parametrize a serie of tropolone derivatives. I can easily assign beads to carbonyl and hydroxyl groups. Initially I assigned two beads for the remaining 5 non-hydrogen atoms. I`m not sure if it was a wise decision. I also cannot find examples of Martini topologies for 7-membered ring. Is it a quite complex molecule to map?
Thanks in advance,

Fred

This image is hidden for guests.
Please log in or register to see it.

Please Log in or Create an account to join the conversation.

More
5 months 2 weeks ago - 5 months 2 weeks ago #9415 by riccardo
Replied by riccardo on topic bead change in martini2 and martini2
Hi, are you using Martini 2 or Martini 3? Assuming you're going for Martini 3 (which I'd recommend, especially for rings), that's how I would go about the mapping (I can't see the image but I'm assuming this is the molecule: en.wikipedia.org/wiki/File:Tropolone.png ): github.com/ricalessandri/Martini3-mappin...b/main/tropolone.pdf
with SN6 for the hydroxyl S-bead and TN6a for the ketone. TC5 for the remaining 2 aromatic T-beads. Note that the S-bead (in green) maps 3 non-hydrogen atoms, so that, excluding the C=0 group, you're left with 4 atoms to be mapped (and hence 2 x T-beads are appropriate).

This follows guidelines and bead type recommendations (Table 1) in onlinelibrary.wiley.com/doi/epdf/10.1002/adts.202100391 . Table 1 can also be found at: github.com/ricalessandri/Martini3-small-...ding_block_table.pdf
Last edit: 5 months 2 weeks ago by riccardo.

Please Log in or Create an account to join the conversation.

  • FJSP22
  • FJSP22's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
5 months 2 weeks ago #9418 by FJSP22
Replied by FJSP22 on topic bead change in martini2 and martini2
Thank you again, Ricardo! I'm using Martini 3. Your beads suggestions seems promising. I'll follow your suggestions.
Thank you so much.

Please Log in or Create an account to join the conversation.

More
4 months 1 week ago #9449 by mathar
Replied by mathar on topic bead change in martini2 and martini2
I am now shifted to martini3 from martini2; looks like ligands parameterized with martini2 are not readable with martini3 force field ??? Are SN5 and TC5e beads changed in martini3?

Please Log in or Create an account to join the conversation.

More
4 months 1 week ago #9455 by riccardo
Replied by riccardo on topic bead change in martini2 and martini2
You cannot mix models between martini 2 and martini 3. The two force fields have a different "balance", it would be like mixing AMBER with OPLS.

Both bead types SN5 and TC5e did not exist in Martini 2.

Please Log in or Create an account to join the conversation.

Time to create page: 0.108 seconds