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Mapping for oleic tails 18:1(9)
- pbuslaev
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7 years 10 months ago #5609
by pbuslaev
Mapping for oleic tails 18:1(9) was created by pbuslaev
Dear all,
I would like to ask if there is a preferred atomistic MARTINI mapping for the oleic acid 18:1(9) ?
Since the "Computational Lipidomics with insane" paper the mapping for this tail group is apparently CDCC, however exact correspondence between the atoms and the beads is not fully clear, and I could not find this information in the publications about MARTINI.
I would like to ask if there is a preferred atomistic MARTINI mapping for the oleic acid 18:1(9) ?
Since the "Computational Lipidomics with insane" paper the mapping for this tail group is apparently CDCC, however exact correspondence between the atoms and the beads is not fully clear, and I could not find this information in the publications about MARTINI.
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- flaviyan
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7 years 10 months ago #5611
by flaviyan
Replied by flaviyan on topic Mapping for oleic tails 18:1(9)
check these pages for the appropriate mapping
cgmartini.nl/index.php/force-field-param...ml?dir=PC&lipid=DOPC
cgmartini.nl/index.php/force-field-param...ml?dir=PC&lipid=DVPC
cgmartini.nl/index.php/force-field-param...ml?dir=PC&lipid=DOPC
cgmartini.nl/index.php/force-field-param...ml?dir=PC&lipid=DVPC
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- pbuslaev
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7 years 10 months ago #5615
by pbuslaev
Replied by pbuslaev on topic Mapping for oleic tails 18:1(9)
Flaviyan, thank you, however these pages, while showing the CG topologies, do not provide the information about full atom to CG mappings, i.e. out of 18 oleoyl carbons, which ones correspond to C1, which ones correspond to D2, and so on?
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- flaviyan
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7 years 10 months ago #5616
by flaviyan
Replied by flaviyan on topic Mapping for oleic tails 18:1(9)
So the new lipid models match the topology for both 16:1 and 18:1 acyl chains and the D2 beads corresponds to the location of the unsaturated bond. The acyl carbons are mapped 4:1 hence in 18:1(9) D2 is the second acyl bad for DOPC, where as in 18:1(11) it's D3 for DVPC.
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- helgi
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7 years 10 months ago - 7 years 10 months ago #5617
by helgi
Replied by helgi on topic Mapping for oleic tails 18:1(9)
Hello, hello,
Our plan is to include backmapping files for the lipids with their .itp’s but as there are so many lipids this has not happened yet. As an example of a mapping of Martini oleic tail to GROMOS united atom model I included the relevant part of a backmapping file for POPC made by Tsjerk (the second column is the AA atom names and the third the Martini bead names).
; Tail 2
22 CGS2 GL1
23 OGS2 GL1 GL1 GL1 C1A
24 CES2 GL1 C1A
25 OES2 GL1
45 C203 C1A
48 C204 C1A C1A C1A D2A
51 C205 C1A D2A
54 C206 D2A D2A D2A C1A
57 C207 D2A
; Double bond
60 C208 D2A D2A C3A
63 C209 C3A C3A D2A
65 C210 C3A C3A D2A
67 C211 C3A C3A C3A D2A
; --
70 C212 C3A
73 C213 C3A C3A C3A C4A
76 C214 C3A C4A
79 C215 C4A C4A C4A C3A
82 C216 C4A
85 C217 C4A
88 C218 C4A
Hope this helps,
Cheers,
- Helgi
Our plan is to include backmapping files for the lipids with their .itp’s but as there are so many lipids this has not happened yet. As an example of a mapping of Martini oleic tail to GROMOS united atom model I included the relevant part of a backmapping file for POPC made by Tsjerk (the second column is the AA atom names and the third the Martini bead names).
; Tail 2
22 CGS2 GL1
23 OGS2 GL1 GL1 GL1 C1A
24 CES2 GL1 C1A
25 OES2 GL1
45 C203 C1A
48 C204 C1A C1A C1A D2A
51 C205 C1A D2A
54 C206 D2A D2A D2A C1A
57 C207 D2A
; Double bond
60 C208 D2A D2A C3A
63 C209 C3A C3A D2A
65 C210 C3A C3A D2A
67 C211 C3A C3A C3A D2A
; --
70 C212 C3A
73 C213 C3A C3A C3A C4A
76 C214 C3A C4A
79 C215 C4A C4A C4A C3A
82 C216 C4A
85 C217 C4A
88 C218 C4A
Hope this helps,
Cheers,
- Helgi
Last edit: 7 years 10 months ago by helgi.
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- pbuslaev
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7 years 10 months ago #5632
by pbuslaev
Replied by pbuslaev on topic Mapping for oleic tails 18:1(9)
Thank you Helgi, this is exactly what I was looking for. Is it possible to get the whole file for any full-atom popc? Or at least for a whole united-atom popc (and maybe dopc and dppc, although I guess I can devise those from popc myself).
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- helgi
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7 years 10 months ago #5634
by helgi
Replied by helgi on topic Mapping for oleic tails 18:1(9)
Yes most of those are available - I put quite a few on the website earlier this week.
e.g. www.cgmartini.nl/index.php/force-field-p...ml?dir=PC&lipid=POPC
DPPC should also be there but not DOPC. We have the x5 bead version but have not updated it to the newer x4 beads yet - if you happen to make the DOPC x4 bead mapping file and willing to share put your name on top of the file and send to us then we can add it to the website.
e.g. www.cgmartini.nl/index.php/force-field-p...ml?dir=PC&lipid=POPC
DPPC should also be there but not DOPC. We have the x5 bead version but have not updated it to the newer x4 beads yet - if you happen to make the DOPC x4 bead mapping file and willing to share put your name on top of the file and send to us then we can add it to the website.
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- pbuslaev
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7 years 10 months ago #5639
by pbuslaev
Replied by pbuslaev on topic Mapping for oleic tails 18:1(9)
Ok, thank you very much!
As I've mentioned earlier, we were interested in the FA to CG mapping, and tried to use backward.py to do it. However, we could not independently reproduce its results. After some looking into the problem, we found the reason. The subroutine "average", which calculates the averaged position of the atoms to obtain the coordinates of the corresponding bead, sometimes does not get the correct masses:
line 39 of __init__.py: mxyz = [(_mass.get(i[0][0],1),i[4],i[5],i[6]) for i in a if i]
Now, i[0][0] returns the first symbol of the atom's name, which is the column 13 of the pdb file. Sometimes the name of the atom is four symbols long, and then i[0][0] gives the correct chemical symbol for it. However, sometimes the atom's name is shorter and starts from the column 14, and then i[0][0] gives the blank character ' ', whose mass is assumed to be 1 (the mass of hydrogen) by the script's code _mass.get(i[0][0],1) This is probably not the expected behavior, but since we aren't very familiar with python scripting, and aren't 100% sure, we cannot correct this ourselves. Should we report this somewhere else?
As for the DOPC mapping, I've sent the file to your rug.nl e-mail adress that was listed on the website.
As I've mentioned earlier, we were interested in the FA to CG mapping, and tried to use backward.py to do it. However, we could not independently reproduce its results. After some looking into the problem, we found the reason. The subroutine "average", which calculates the averaged position of the atoms to obtain the coordinates of the corresponding bead, sometimes does not get the correct masses:
line 39 of __init__.py: mxyz = [(_mass.get(i[0][0],1),i[4],i[5],i[6]) for i in a if i]
Now, i[0][0] returns the first symbol of the atom's name, which is the column 13 of the pdb file. Sometimes the name of the atom is four symbols long, and then i[0][0] gives the correct chemical symbol for it. However, sometimes the atom's name is shorter and starts from the column 14, and then i[0][0] gives the blank character ' ', whose mass is assumed to be 1 (the mass of hydrogen) by the script's code _mass.get(i[0][0],1) This is probably not the expected behavior, but since we aren't very familiar with python scripting, and aren't 100% sure, we cannot correct this ourselves. Should we report this somewhere else?
As for the DOPC mapping, I've sent the file to your rug.nl e-mail adress that was listed on the website.
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- tsjerk
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7 years 10 months ago #5643
by tsjerk
Replied by tsjerk on topic Mapping for oleic tails 18:1(9)
Right. Thanks for nailing this. If you set it to i[0][1] it should work for your purpose, as the PDB format should have the element in columns 13/14, right aligned, so the one letter elements are put in column 14. Hydrogen is a bit special, as there may be so many that the name needs four characters, but the suggested fix will assign them a mass of 1. I probably assumed that the atom names was stripped of leading spaces, but it appears not to be. We'll work on a better solution to make backward better suited for forward mapping.
-Tsjerk
-Tsjerk
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- Mel
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7 years 10 months ago #5666
by Mel
Replied by Mel on topic Mapping for oleic tails 18:1(9)
Hi,
I have a question: How did you produce the DOPC AA topology?
I have a question: How did you produce the DOPC AA topology?
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- pbuslaev
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7 years 10 months ago #5697
by pbuslaev
Replied by pbuslaev on topic Mapping for oleic tails 18:1(9)
Hi Mel,
I'm not sure if the question is about AA topology or mapping. The AA topology is standard for CHARMM36. For mapping, I took the POPC file (available here www.cgmartini.nl/index.php/force-field-p...ml?dir=PC&lipid=POPC ) as a template and copied the oleoil mapping for the DOPC's second chain (C1B-D2B-C3B-C4B) from that of POPC's first chain (C1A-D2A-C3A-C4A). So, the mappings for both DOPC oleoils are assumed to be the same, and identical to the mapping of POPC's oleoil
I'm not sure if the question is about AA topology or mapping. The AA topology is standard for CHARMM36. For mapping, I took the POPC file (available here www.cgmartini.nl/index.php/force-field-p...ml?dir=PC&lipid=POPC ) as a template and copied the oleoil mapping for the DOPC's second chain (C1B-D2B-C3B-C4B) from that of POPC's first chain (C1A-D2A-C3A-C4A). So, the mappings for both DOPC oleoils are assumed to be the same, and identical to the mapping of POPC's oleoil
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- Mel
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7 years 10 months ago - 7 years 10 months ago #5700
by Mel
Replied by Mel on topic Mapping for oleic tails 18:1(9)
Hi,
thank you pbuslaev, that was the answer I was looking for.
I am still not sure why in the CHARMM36 file the H-atom of the C10 is part of the D2 bead but the C10 atom itself is in the C3 bead.
What column corresponds to the CG beads?
As for the Gromos file: why is the double bond between C7 and C8 and not C9 and C10?
Thank you again for your help.
Mel
thank you pbuslaev, that was the answer I was looking for.
I am still not sure why in the CHARMM36 file the H-atom of the C10 is part of the D2 bead but the C10 atom itself is in the C3 bead.
What column corresponds to the CG beads?
As for the Gromos file: why is the double bond between C7 and C8 and not C9 and C10?
Thank you again for your help.
Mel
Last edit: 7 years 10 months ago by Mel.
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- pbuslaev
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7 years 9 months ago #5707
by pbuslaev
Replied by pbuslaev on topic Mapping for oleic tails 18:1(9)
As far as I understand this mapping data would be better viewed as "position of the bead D2 is a better initial approximation for the position of H-atom of the C10, and position of the bead C3 is a better initial approximation for the position of the C10 atom itself". This is described in the article about backward.py (
pubs.acs.org/doi/abs/10.1021/ct400617g
) and can be deduced from the script itself.
Regarding the gromos file, position of the double bond is defined in the force field topology file and not in the backward.py mapping file. The comment in the backward.py mapping file probably highlights the fact that atoms of the double bond dihedral angle definition are situated below - but it is better to ask the author of the file.
Regarding the gromos file, position of the double bond is defined in the force field topology file and not in the backward.py mapping file. The comment in the backward.py mapping file probably highlights the fact that atoms of the double bond dihedral angle definition are situated below - but it is better to ask the author of the file.
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- Mel
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7 years 9 months ago #5747
by Mel
Replied by Mel on topic Mapping for oleic tails 18:1(9)
Ah, thanks pbuslaev for the clarification.
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