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How to perform the mapping of GLYCERINE molecule?
- ncfm
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8 years 5 months ago #5264
by ncfm
How to perform the mapping of GLYCERINE molecule? was created by ncfm
Hello,
I was performing the mapping of GLYCERINE molecule CH2(OH).
The first segment is ok as with 1 sphere of -CH(OH)-CH2(OH) : (OH-C2-OH): P4 type
I have doubt about the mapping of second segment (-C-OH) : ?
Kindly provide guidance for the mapping of the same
Thank you...
I was performing the mapping of GLYCERINE molecule CH2(OH).
The first segment is ok as with 1 sphere of -CH(OH)-CH2(OH) : (OH-C2-OH): P4 type
I have doubt about the mapping of second segment (-C-OH) : ?
Kindly provide guidance for the mapping of the same
Thank you...
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- helgi
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8 years 4 months ago #5282
by helgi
Replied by helgi on topic How to perform the mapping of GLYCERINE molecule?
Sadly there is no correct answer to this question.
Using the Martini 4:1 regular mapping, this molecule is too larger for x1 bead and too little for x2. The glycerol-linked lipids have x2 beads (GL1 and GL2) for the linker but those are also considered to include the first carbon from each fatty acid tail.
I would try to preserve the symmetry of the molecule, e.g. have x2 s-breads with both sharing the central C-OH. I would also do AA simulations to get the bonds / angles and to measure the solvation free energy e.g. water / octanol and from that you can pick the bead type (most likely something like SP3).
Hope this helps,
Cheers,
- Helgi
Using the Martini 4:1 regular mapping, this molecule is too larger for x1 bead and too little for x2. The glycerol-linked lipids have x2 beads (GL1 and GL2) for the linker but those are also considered to include the first carbon from each fatty acid tail.
I would try to preserve the symmetry of the molecule, e.g. have x2 s-breads with both sharing the central C-OH. I would also do AA simulations to get the bonds / angles and to measure the solvation free energy e.g. water / octanol and from that you can pick the bead type (most likely something like SP3).
Hope this helps,
Cheers,
- Helgi
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