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Sitosterol Parameters in Martini 3
- Joufflu
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11 months 4 days ago #9640
by Joufflu
Sitosterol Parameters in Martini 3 was created by Joufflu
Hi Martini Community,
I'm rather new to this field, but I've recently ventured into identifying sitosterol pubchem in Martini 3. I've used the cholesterol parameters from this study as a guide: github.com/Martini-Force-Field-Initiative/M3-Sterol-Parameters .
With this as my reference, I took a shot at creating an ITP file for sitosterol. However, I'm very aware of my novice status and I am unsure about the correctness of my approach.
If any of you experts could spare some time to take a glance at my methodology and provide any suggestions or corrections, I would be immensely grateful.
Thank you in advance for your patience and help.
Best ,
Joufflu
Sitosterol ITP test file :
; MARTINI 3 Sisterol Version 1.0 (may 2023)
;
; Martini 3 topology of Sisterol.
;
; Warning(s)/Note(s):
; Add define=-DFLEXIBLE to select harmonic bonds for minimization purposes.
;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;
; When using these parameters please read and cite the parameterization article:
; Borges-Araújo, L. et al. Martini 3 Coarse-Grained Force Field for SITOesterol. (2023) doi:10.26434/chemrxiv-2023-lh7bq
;
; Also be sure to check github.com/Martini-Force-Field-Initiative/M3-Sterol-Parameters
; for updates to these parameters.
;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
[ moleculetype ]
; molname nrexcl
SITO 1
[ atoms ]
; i type resnr residue atom cgnr charge mass
1 P1 1 SITO ROH 1 0.0 0.0
2 SC4 1 SITO R1 2 0.0 159.8
3 SC3 1 SITO R2 3 0.0 157.0
4 SC3 1 SITO R3 4 0.0 0.0
5 SC3 1 SITO R4 5 0.0 0.0
6 TC2 1 SITO R5 6 0.0 0.0
7 TC2 1 SITO R6 7 0.0 0.0
8 C2 1 SITO C1 8 0.0 115.2
9 C2 1 SITO C2 9 0.0 72.0
10 C1 1 SITO C3 10 0.0 72.0 ; added
[ bonds ]
; i j funct length force
8 9 1 0.440 15000
9 10 1 0.440 15000.0 ; added
#ifdef FLEXIBLE
8 3 1 0.75012 100000
8 2 1 0.78504 100000
3 2 1 0.34797 100000
#else
[ constraints ]
8 3 1 0.75012
8 2 1 0.78504
3 2 1 0.34797
#endif
[ angles ]
; i j k funct angle force
; SITOesterol acyl chain angle
5 4 9 1 99.0 250 ;R4-R3-C2
8 9 10 1 109.5 500 ; added
[ dihedrals ]
; i j k l funct angle force
; SITOesterol acyl chain tortion
7 5 4 9 2 -70.0 50 ;R6-R4-R3-C2
7 8 9 10 2 -70.0 50 ;R6-C1-C2-C3 ; added
[ virtual_sites3 ]
1 8 3 2 4 1.08999 0.35891 0.22947
4 8 3 2 4 -0.41067 0.83597 -0.05311
5 8 3 2 4 0.69138 -0.10352 0.17476
6 8 3 2 4 0.77524 0.22413 0.92700
7 8 3 2 4 0.06219 0.32398 0.76967
[ exclusions ]
; i j k ...
1 2 3 4 5 6 7 8 ;added 9 to each line and added one line to the end
2 3 4 5 6 7 8 9
3 4 5 6 7 8 9
4 5 6 7 8 9
5 6 7 8 9
6 7 8 9
7 8 9
8 9
I'm rather new to this field, but I've recently ventured into identifying sitosterol pubchem in Martini 3. I've used the cholesterol parameters from this study as a guide: github.com/Martini-Force-Field-Initiative/M3-Sterol-Parameters .
With this as my reference, I took a shot at creating an ITP file for sitosterol. However, I'm very aware of my novice status and I am unsure about the correctness of my approach.
If any of you experts could spare some time to take a glance at my methodology and provide any suggestions or corrections, I would be immensely grateful.
Thank you in advance for your patience and help.
Best ,
Joufflu
Sitosterol ITP test file :
; MARTINI 3 Sisterol Version 1.0 (may 2023)
;
; Martini 3 topology of Sisterol.
;
; Warning(s)/Note(s):
; Add define=-DFLEXIBLE to select harmonic bonds for minimization purposes.
;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;
; When using these parameters please read and cite the parameterization article:
; Borges-Araújo, L. et al. Martini 3 Coarse-Grained Force Field for SITOesterol. (2023) doi:10.26434/chemrxiv-2023-lh7bq
;
; Also be sure to check github.com/Martini-Force-Field-Initiative/M3-Sterol-Parameters
; for updates to these parameters.
;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
[ moleculetype ]
; molname nrexcl
SITO 1
[ atoms ]
; i type resnr residue atom cgnr charge mass
1 P1 1 SITO ROH 1 0.0 0.0
2 SC4 1 SITO R1 2 0.0 159.8
3 SC3 1 SITO R2 3 0.0 157.0
4 SC3 1 SITO R3 4 0.0 0.0
5 SC3 1 SITO R4 5 0.0 0.0
6 TC2 1 SITO R5 6 0.0 0.0
7 TC2 1 SITO R6 7 0.0 0.0
8 C2 1 SITO C1 8 0.0 115.2
9 C2 1 SITO C2 9 0.0 72.0
10 C1 1 SITO C3 10 0.0 72.0 ; added
[ bonds ]
; i j funct length force
8 9 1 0.440 15000
9 10 1 0.440 15000.0 ; added
#ifdef FLEXIBLE
8 3 1 0.75012 100000
8 2 1 0.78504 100000
3 2 1 0.34797 100000
#else
[ constraints ]
8 3 1 0.75012
8 2 1 0.78504
3 2 1 0.34797
#endif
[ angles ]
; i j k funct angle force
; SITOesterol acyl chain angle
5 4 9 1 99.0 250 ;R4-R3-C2
8 9 10 1 109.5 500 ; added
[ dihedrals ]
; i j k l funct angle force
; SITOesterol acyl chain tortion
7 5 4 9 2 -70.0 50 ;R6-R4-R3-C2
7 8 9 10 2 -70.0 50 ;R6-C1-C2-C3 ; added
[ virtual_sites3 ]
1 8 3 2 4 1.08999 0.35891 0.22947
4 8 3 2 4 -0.41067 0.83597 -0.05311
5 8 3 2 4 0.69138 -0.10352 0.17476
6 8 3 2 4 0.77524 0.22413 0.92700
7 8 3 2 4 0.06219 0.32398 0.76967
[ exclusions ]
; i j k ...
1 2 3 4 5 6 7 8 ;added 9 to each line and added one line to the end
2 3 4 5 6 7 8 9
3 4 5 6 7 8 9
4 5 6 7 8 9
5 6 7 8 9
6 7 8 9
7 8 9
8 9
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- neubergm
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11 months 4 days ago #9643
by neubergm
Replied by neubergm on topic Sitosterol Parameters in Martini 3
Hi Joufflu,
I've recently started working on M3 sitosterol as well. Nevertheless I have barely any experience with parametrizing a new molecule as well, so I am happy you've opened the discussion.
Same as you I've used cholesterol as a reference. But than I've added TC1 bead, since tiny bead should be used to replace 2 heavy beads (I guess that's our case) according to the M3 source publication.
10 TC1 1 SITO C3 10 0.0 36.0
Than I am just wondering how you've set up the angles and force constants, because these are crutial and I am strugling with them a lot. I would like to use AA simulation as a reference, but so far without any success.
Hope we will figure it out!
Michaela
I've recently started working on M3 sitosterol as well. Nevertheless I have barely any experience with parametrizing a new molecule as well, so I am happy you've opened the discussion.
Same as you I've used cholesterol as a reference. But than I've added TC1 bead, since tiny bead should be used to replace 2 heavy beads (I guess that's our case) according to the M3 source publication.
10 TC1 1 SITO C3 10 0.0 36.0
Than I am just wondering how you've set up the angles and force constants, because these are crutial and I am strugling with them a lot. I would like to use AA simulation as a reference, but so far without any success.
Hope we will figure it out!
Michaela
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- Joufflu
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10 months 3 weeks ago #9650
by Joufflu
Replied by Joufflu on topic Sitosterol Parameters in Martini 3
Dear Michaela,
Thank you so much for your message.I'm delighted to see that you're also working on M3 sitosterol.
Firstly, I want to express my gratitude for suggesting the TC1 bead. I believe it's a great idea to use a small bead to replace two heavy beads, as mentioned in the M3 source publication.
Regarding the angles and force constants, I'm facing the same challenges as you are. I recently came across an article titled "Automatic Optimization of Lipid Models in the Martini Force Field Using SwarmCG." It proposes a method for parameterizing based on all-atom simulations. I believe it could be an interesting avenue to explore. Unfortunately, I haven't had the time to launch all-atom simulations yet.
Once again, thank you for your message and your valuable contribution to this discussion.
Best regards,
Thank you so much for your message.I'm delighted to see that you're also working on M3 sitosterol.
Firstly, I want to express my gratitude for suggesting the TC1 bead. I believe it's a great idea to use a small bead to replace two heavy beads, as mentioned in the M3 source publication.
Regarding the angles and force constants, I'm facing the same challenges as you are. I recently came across an article titled "Automatic Optimization of Lipid Models in the Martini Force Field Using SwarmCG." It proposes a method for parameterizing based on all-atom simulations. I believe it could be an interesting avenue to explore. Unfortunately, I haven't had the time to launch all-atom simulations yet.
Once again, thank you for your message and your valuable contribution to this discussion.
Best regards,
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