- Posts: 10
Methyl group in a lipidic tail
- Prunotto
-
Topic Author
- Offline
- Fresh Boarder
Less
More
8 years 5 months ago #5248
by Prunotto
Methyl group in a lipidic tail was created by Prunotto
Dear all,
I am parameterizing a lipid that is not present in the MARTINI database.
The tails of this lipid are basically two stearoyl acids (chains composed by 18 saturated carbons). I see from your website ( www.cgmartini.nl/index.php/force-field-p...s2/350-lipid-details ) that in this case I should use 4 'C' particles in a row for each tail.
However, these chains also present a methyl group at the 11th carbon atom.
I looked carefully, but I could not find any clue on how to model a methyl group in MARTINI. I understand that probably I will not need to add any particle to my MARTINI model, but would I need to slightly change my parameters in order to take into account the presence of the methyl group?
Looking forward to receiving your reply!
All the best,
Alessio
I am parameterizing a lipid that is not present in the MARTINI database.
The tails of this lipid are basically two stearoyl acids (chains composed by 18 saturated carbons). I see from your website ( www.cgmartini.nl/index.php/force-field-p...s2/350-lipid-details ) that in this case I should use 4 'C' particles in a row for each tail.
However, these chains also present a methyl group at the 11th carbon atom.
I looked carefully, but I could not find any clue on how to model a methyl group in MARTINI. I understand that probably I will not need to add any particle to my MARTINI model, but would I need to slightly change my parameters in order to take into account the presence of the methyl group?
Looking forward to receiving your reply!
All the best,
Alessio
Please Log in or Create an account to join the conversation.
- helgi
-
- Offline
- Administrator
Less
More
- Posts: 54
8 years 5 months ago #5250
by helgi
Replied by helgi on topic Methyl group in a lipidic tail
When you say “methyl group at the 11th carbon atom” I am assuming you have a branched lipid tail at that position?
If so those are unfortunately a little tricky, we are currently looking into how best to represent branched tail lipids but have not finalized that work yet. Normally if you add a methyl group you would change the bead type to represent the increased hydrophobicity but there is no available Martini bead type that is more hydrophobicity than the current C1 bead. More importantly you would have to change the angle over that bead, adding the methyl group will disrupt the H bonding down the lipid tail, effectively putting a kink in the tail (similarly to adding a double bond but not the same). To get that angle correct you could simulate the lipid atomistically map the AA trajectory to CG and measure the angle. You might have to iterate the CG topology a few times until you get a good match between the angle distributions.
Hope this helps,
Cheers,
- Helgi
If so those are unfortunately a little tricky, we are currently looking into how best to represent branched tail lipids but have not finalized that work yet. Normally if you add a methyl group you would change the bead type to represent the increased hydrophobicity but there is no available Martini bead type that is more hydrophobicity than the current C1 bead. More importantly you would have to change the angle over that bead, adding the methyl group will disrupt the H bonding down the lipid tail, effectively putting a kink in the tail (similarly to adding a double bond but not the same). To get that angle correct you could simulate the lipid atomistically map the AA trajectory to CG and measure the angle. You might have to iterate the CG topology a few times until you get a good match between the angle distributions.
Hope this helps,
Cheers,
- Helgi
Please Log in or Create an account to join the conversation.
- Prunotto
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 10
8 years 5 months ago #5252
by Prunotto
Replied by Prunotto on topic Methyl group in a lipidic tail
Yes, that's exactly what I meant. Sorry, my terminology is not very proper, but I am not a chemist, therefore I'm learning as I go :)
Thank you very much for your suggestions, they were very precious!
Thank you very much for your suggestions, they were very precious!
Please Log in or Create an account to join the conversation.
Time to create page: 0.100 seconds