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Regarding DPGG MARTINI parameters
- Navarro
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8 years 9 months ago - 8 years 9 months ago #4721
by Navarro
Regarding DPGG MARTINI parameters was created by Navarro
Dear MARTINI users,
I just realized that in the parameters of the DPGG lipid in md.chem.rug.nl/cgmartini/index.php/force...ld-parameters/lipids ,regarding to the bond interactions four are commented
[ bonds ]
; ai aj funct c0 c1 c2 c3
; 1 2 1 0.3 30000
; 1 3 1 0.3 30000
1 4 1 0.44 10000
; 4 5 1 0.3 30000
; 5 6 1 0.3 30000
5 7 1 0.5 10000
7 8 1 0.37 1250
7 9 1 0.47 1250
9 10 1 0.470 1250
10 11 1 0.470 1250
11 12 1 0.470 1250
8 13 1 0.470 1250
13 14 1 0.470 1250
14 15 1 0.470 1250
15 16 1 0.470 1250
Is there an specific reason for that? Why not delete them in the first place? Can i use this parameters without worrying about the results i can get with them?
Thanks in advance,
Carlos
I just realized that in the parameters of the DPGG lipid in md.chem.rug.nl/cgmartini/index.php/force...ld-parameters/lipids ,regarding to the bond interactions four are commented
[ bonds ]
; ai aj funct c0 c1 c2 c3
; 1 2 1 0.3 30000
; 1 3 1 0.3 30000
1 4 1 0.44 10000
; 4 5 1 0.3 30000
; 5 6 1 0.3 30000
5 7 1 0.5 10000
7 8 1 0.37 1250
7 9 1 0.47 1250
9 10 1 0.470 1250
10 11 1 0.470 1250
11 12 1 0.470 1250
8 13 1 0.470 1250
13 14 1 0.470 1250
14 15 1 0.470 1250
15 16 1 0.470 1250
Is there an specific reason for that? Why not delete them in the first place? Can i use this parameters without worrying about the results i can get with them?
Thanks in advance,
Carlos
Last edit: 8 years 9 months ago by Navarro.
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- floris
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8 years 9 months ago #4722
by floris
Replied by floris on topic Regarding DPGG MARTINI parameters
Hello Carlos,
Well noticed!
But if you scroll a bit down you can seen that the commented bonds have been replaced by constraints, which are basically a kind of super strong bonds.
You can just use this topology without problems.
But please be aware that there is an updated version of this headgroup available!
This can be found in the lipids OPGG, DFGG and FPGG. By combining the headgropu of these topologies with the DPGG tails you can construct a DPGG lipid with updated headgroup. Be aware that the order of the beads is different in the DPPG and the OPGG, DFGG and FPGG headgroups!
Good luck!
Floris
Well noticed!
But if you scroll a bit down you can seen that the commented bonds have been replaced by constraints, which are basically a kind of super strong bonds.
You can just use this topology without problems.
But please be aware that there is an updated version of this headgroup available!
This can be found in the lipids OPGG, DFGG and FPGG. By combining the headgropu of these topologies with the DPGG tails you can construct a DPGG lipid with updated headgroup. Be aware that the order of the beads is different in the DPPG and the OPGG, DFGG and FPGG headgroups!
Good luck!
Floris
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- Navarro
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8 years 8 months ago #4747
by Navarro
Replied by Navarro on topic Regarding DPGG MARTINI parameters
Hi Floris,
Thanks a lot for your reply.
I tried to combine the two topologies (the update headgroup from your work and the tails parameters from OPGG), getting this:
[ moleculetype ]
DPGG 1
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
1 SP2 1 DPGG GB2 5 0 72
2 P4 1 DPGG GB3 6 0 72
3 SN0 1 DPGG GB1 4 0 72
4 SP2 1 DPGG GA1 1 0 72
5 P4 1 DPGG GA2 2 0 72
6 P1 1 DPGG GA3 3 0 72
7 Na 1 DPGG GL1 4 0 72
8 Na 1 DPGG GL2 5 0 72
9 C1 1 DPGG C1A 6 0 72
10 C1 1 DPGG C2A 7 0 72
11 C1 1 DPGG C3A 8 0 72
12 C1 1 DPGG C4A 9 0 72
13 C1 1 DPGG C1B 10 0 72
14 C1 1 DPGG C2B 11 0 72
15 C1 1 DPGG C3B 12 0 72
16 C1 1 DPGG C4B 13 0 72
[ bonds ]
; ai aj funct c0 c1 c2 c3
4 5 1 0.3 30000
4 6 1 0.3 30000
4 3 1 0.44 10000
3 1 1 0.3 30000
1 2 1 0.3 30000
1 7 1 0.5 10000
7 8 1 0.37 1250
7 9 1 0.47 1250
9 10 1 0.470 1250
10 11 1 0.470 1250
11 12 1 0.470 1250
8 13 1 0.470 1250
13 14 1 0.470 1250
14 15 1 0.470 1250
15 16 1 0.470 1250
[ angles ]
; ai aj ak funct c0 c1 c2 c3
5 4 3 2 81.00 35.00
6 4 3 2 100.00 35.00
1 3 4 2 180.00 35.00
1 7 8 2 100.00 35.00
2 1 7 2 106.00 35.00
1 7 9 2 150.00 35.00
7 9 10 2 180.00 25.00
9 10 11 2 180.00 25.00
10 11 12 2 180.00 25.00
8 13 14 2 180.00 25.00
13 14 15 2 180.00 25.00
14 15 16 2 180.00 25.00
[ dihedrals ]
5 4 3 1 1 -20.00 5.00 1
3 1 7 9 1 -80.00 5.00 1
[ constraints ]
4 5 1 0.3
4 6 1 0.3
3 1 1 0.3
1 2 1 0.3
[ exclusions ]
3 2
Is this ok?
Regarding the differences between OPGG and DPGG, this were the c0 and c1 values in 13 14 15 2 180.00 25.00 , values, right? from 120.00 and 45.00 in OPGG to 180.00 and 25.00 in DPGG respectively?
Best,
Carlos
Thanks a lot for your reply.
I tried to combine the two topologies (the update headgroup from your work and the tails parameters from OPGG), getting this:
[ moleculetype ]
DPGG 1
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
1 SP2 1 DPGG GB2 5 0 72
2 P4 1 DPGG GB3 6 0 72
3 SN0 1 DPGG GB1 4 0 72
4 SP2 1 DPGG GA1 1 0 72
5 P4 1 DPGG GA2 2 0 72
6 P1 1 DPGG GA3 3 0 72
7 Na 1 DPGG GL1 4 0 72
8 Na 1 DPGG GL2 5 0 72
9 C1 1 DPGG C1A 6 0 72
10 C1 1 DPGG C2A 7 0 72
11 C1 1 DPGG C3A 8 0 72
12 C1 1 DPGG C4A 9 0 72
13 C1 1 DPGG C1B 10 0 72
14 C1 1 DPGG C2B 11 0 72
15 C1 1 DPGG C3B 12 0 72
16 C1 1 DPGG C4B 13 0 72
[ bonds ]
; ai aj funct c0 c1 c2 c3
4 5 1 0.3 30000
4 6 1 0.3 30000
4 3 1 0.44 10000
3 1 1 0.3 30000
1 2 1 0.3 30000
1 7 1 0.5 10000
7 8 1 0.37 1250
7 9 1 0.47 1250
9 10 1 0.470 1250
10 11 1 0.470 1250
11 12 1 0.470 1250
8 13 1 0.470 1250
13 14 1 0.470 1250
14 15 1 0.470 1250
15 16 1 0.470 1250
[ angles ]
; ai aj ak funct c0 c1 c2 c3
5 4 3 2 81.00 35.00
6 4 3 2 100.00 35.00
1 3 4 2 180.00 35.00
1 7 8 2 100.00 35.00
2 1 7 2 106.00 35.00
1 7 9 2 150.00 35.00
7 9 10 2 180.00 25.00
9 10 11 2 180.00 25.00
10 11 12 2 180.00 25.00
8 13 14 2 180.00 25.00
13 14 15 2 180.00 25.00
14 15 16 2 180.00 25.00
[ dihedrals ]
5 4 3 1 1 -20.00 5.00 1
3 1 7 9 1 -80.00 5.00 1
[ constraints ]
4 5 1 0.3
4 6 1 0.3
3 1 1 0.3
1 2 1 0.3
[ exclusions ]
3 2
Is this ok?
Regarding the differences between OPGG and DPGG, this were the c0 and c1 values in 13 14 15 2 180.00 25.00 , values, right? from 120.00 and 45.00 in OPGG to 180.00 and 25.00 in DPGG respectively?
Best,
Carlos
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- floris
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8 years 8 months ago - 8 years 8 months ago #4749
by floris
Replied by floris on topic Regarding DPGG MARTINI parameters
Ciao Carlos,
Unfortunately I do not have enough time to double check your topology, but there are a few important thinks to keep in mind:
1) if you use insane, to make your membrane patch, please make sure that the order of the beads corrsponds to the one that insane uses. Especially the GG headgroups are tricky! That is why the order of the headgroup beads is different among the GG headgroups published and those used for the thylakoid paper.
2) the connection between the headgroup and the tails. Usually the GL1 bead is linked to the Sn2 tail and the GL2 bead to the SN1 tail. So double check this!
3) do not define both constraints and bonds on the same bond. --> normally you use either bonds or constraints. Not both.
I can see that at least point two and point three are incorrect, (although to be honest, since your tails are identical, it is not a really big prolem this time, however I would strongly suggest you to still change it the correct way!!!)
You also defined an exclusions between bead two and three, please be aware that this is from old parameters!!!! Unless you really wanna use them, please use the updated topologies (from eg DFGG)
As described in the martini paper,
a palmitoyl bond has an angle of 180 degrees with Fc of 25, and a oleoyl of 120 degrees with an fc of 45
Floris
Unfortunately I do not have enough time to double check your topology, but there are a few important thinks to keep in mind:
1) if you use insane, to make your membrane patch, please make sure that the order of the beads corrsponds to the one that insane uses. Especially the GG headgroups are tricky! That is why the order of the headgroup beads is different among the GG headgroups published and those used for the thylakoid paper.
2) the connection between the headgroup and the tails. Usually the GL1 bead is linked to the Sn2 tail and the GL2 bead to the SN1 tail. So double check this!
3) do not define both constraints and bonds on the same bond. --> normally you use either bonds or constraints. Not both.
I can see that at least point two and point three are incorrect, (although to be honest, since your tails are identical, it is not a really big prolem this time, however I would strongly suggest you to still change it the correct way!!!)
You also defined an exclusions between bead two and three, please be aware that this is from old parameters!!!! Unless you really wanna use them, please use the updated topologies (from eg DFGG)
As described in the martini paper,
a palmitoyl bond has an angle of 180 degrees with Fc of 25, and a oleoyl of 120 degrees with an fc of 45
Floris
Last edit: 8 years 8 months ago by floris.
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