normal Bead division problem

  • Hot
  • Hot's Avatar Topic Author
  • Visitor
4 years 6 months ago - 4 years 6 months ago #8262 by Hot
Bead division problem was created by Hot
I used auto-martini tool to partition the molecules and found that some of the beads were not 4-1 or 3-1 mappings,the results are as follows:

[atoms]
; id type resnr residu atom cgnr charge smiles
1 SC5 1 HCB2 S01 1 0 ; [H]c1cc([H])c([H])c([H])c1[H]
2 SC5 1 HCB2 S02 2 0 ; [H]c1cc([H])c([H])c([H])c1[H]
3 SC5 1 HCB2 S03 3 0 ; [H]c1cc([H])c([H])c([H])c1[H]
4 P1 1 HCB2 P01 4 0 ; OC=O
5 P1 1 HCB2 P02 5 0 ; [H]OC([H])([H])OC([H])([H])C([H])[H]


I wonder if this division is possible.
Last edit: 4 years 6 months ago by Hot. Reason: I can not see it

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

More
4 years 6 months ago #8263 by peterkroon
Replied by peterkroon on topic Bead division problem
Hi Hot,

Let's first make sure we're talking about the same molecule. Could you post the SMILES string you used? In the meantime I'll go ahead and guess it's this: C1=CC=CC=C1C(=O)OCCOCO

This molecule is hard to map. The mapping proposed by automartini is not bad. By hand I would probably add one more CH2 group to bead P01 (OC=O).

Do note that automartini was not made by our group, so I can't go much more in depth as to why it proposes this mapping, or how to correct it using automartini.

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

  • Hot
  • Hot's Avatar Topic Author
  • Visitor
4 years 6 months ago - 4 years 6 months ago #8264 by Hot
Replied by Hot on topic Bead division problem
SMILES:c1cc(ccc1)C(=O)OCCOCO
In fact, it is a repetitive unit of polyester fibers(PET).
According the auto-martini, if PET:OCCOC(=O)c1ccc(cc1)C(=O)OCCOC(=O)c1ccc(cc1)C(=O)OCCOC(=O)c1ccc(cc1)C(=O)O,
it could be P2 SC5 SC5 SC5 P1 P1 SC5 SC5 SC5 P1 P1 SC5 SC5 SC5 P1.
P2:[H]OC([H])([H])C([H])[H]OC=O
There may be 3-1, 4-1,5-1,6-1 in one molecule.
Last edit: 4 years 6 months ago by Hot. Reason: add words

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

More
4 years 6 months ago #8265 by peterkroon
Replied by peterkroon on topic Bead division problem
Don't use a tool to make beads for something that's obviously repeating. They'll probably get it wrong.

If I were you I'd take one repeat unit (e.g. ~COC(=O)c1ccc(cc1)C(=O)OC~; there's multiple options) and come up with a mapping and parameters for that.
Finally you'll need to spend some brain cycles to figure out what parameters you need to stitch those repeat units together, and what to do with the termini, but I'm sure you'll manage :)

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

  • Hot
  • Hot's Avatar Topic Author
  • Visitor
4 years 6 months ago #8267 by Hot
Replied by Hot on topic Bead division problem
Thanks for your advice, I will try different mappings and parameters.

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

Time to create page: 0.101 seconds