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Martini lipid itp generator
- z.sichaib
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4 years 8 months ago #8212
by z.sichaib
Martini lipid itp generator was created by z.sichaib
Dear Martini users,
I want to build a membrane containing the following phospholipids, among others:
PE 18:0/22:6
PS 18:0/22:6
PI 18:0/20:4
There are no itp files of these lipids in the website. Thus I am using "lipid-martini-itp-v06.py" to generate them.
With python lipid-martini-itp-v06.py -h I get:
...
"DDDDDD DDDDDD" - C22:6(4c,7c,10c,13c,16c,19c) - diDocosahexaenoyl
...
But when I check one of the itp files in the website, for example, C16:0/22:6 PC (PUPC), there is:
; The Martini lipid itp generator version 0.4 Args are: -o martini_v2.0_PUPC_01.itp -alname PUPC -alhead 'C P' -allink 'G G' -altail 'DDDDD CCCC'
In the itp file of PUPC the lipid tail 22:6 is represented with 5 D beads, whereas in the description of lipid itp generator file it is represented by 6 D beads!
Something is wrong here I guess?
According to the description, D bead corresponds to (CH2-CH=CH-CH2). If I represent the lipid tail 22:6 with 5 D beads it's the equivalent of a chain of 20 carbons. However, if I represent it with 6 D beads, it's equivalent to 24 beads!! ... I am confused... What is the correct description of the tail 22:6 that I should use?
Another question regarding the Cardiolipin itp files on the website. Unless I missed it, I can't find the type of cardiolipin that is represented in that file. I guess it is CL (18:1)x4. Is it correct?
Thank you in advance for your help.
Zeineb
I want to build a membrane containing the following phospholipids, among others:
PE 18:0/22:6
PS 18:0/22:6
PI 18:0/20:4
There are no itp files of these lipids in the website. Thus I am using "lipid-martini-itp-v06.py" to generate them.
With python lipid-martini-itp-v06.py -h I get:
...
"DDDDDD DDDDDD" - C22:6(4c,7c,10c,13c,16c,19c) - diDocosahexaenoyl
...
But when I check one of the itp files in the website, for example, C16:0/22:6 PC (PUPC), there is:
; The Martini lipid itp generator version 0.4 Args are: -o martini_v2.0_PUPC_01.itp -alname PUPC -alhead 'C P' -allink 'G G' -altail 'DDDDD CCCC'
In the itp file of PUPC the lipid tail 22:6 is represented with 5 D beads, whereas in the description of lipid itp generator file it is represented by 6 D beads!
Something is wrong here I guess?
According to the description, D bead corresponds to (CH2-CH=CH-CH2). If I represent the lipid tail 22:6 with 5 D beads it's the equivalent of a chain of 20 carbons. However, if I represent it with 6 D beads, it's equivalent to 24 beads!! ... I am confused... What is the correct description of the tail 22:6 that I should use?
Another question regarding the Cardiolipin itp files on the website. Unless I missed it, I can't find the type of cardiolipin that is represented in that file. I guess it is CL (18:1)x4. Is it correct?
Thank you in advance for your help.
Zeineb
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- xavier
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4 years 8 months ago #8220
by xavier
Replied by xavier on topic Martini lipid itp generator
Hi,
I am not familiar with the script "lipid-martini-itp-v06.py" but what you describe reflects an important issue in the Martini lipid tail representation and CGing in general. That is because Martini represents about 4 heavy atoms per CG bead you can, in theory, only model tails that have a number of C multiple of 4. This is relatively limiting so compromises have to be made.
22:6 is a typical example of that issue. I do not think that a proper parameterization of the poly-unsaturated chains have been made, but I might be wrong. The 5 vs 6 beads might be that originally a 6 beads was used but was found a little too long compared to atomistic models but I can really remember.
I do remember using them for a project some time ago and we realized that multiple D beads in a tail was increasing their attraction to proteins and themselves a little more than expected but we did not really have exp data. The project never got to an end :((.
I would think that a 5 beads might be ok but be careful with the interaction strength, not thoroughly tested!
I am not familiar with the script "lipid-martini-itp-v06.py" but what you describe reflects an important issue in the Martini lipid tail representation and CGing in general. That is because Martini represents about 4 heavy atoms per CG bead you can, in theory, only model tails that have a number of C multiple of 4. This is relatively limiting so compromises have to be made.
22:6 is a typical example of that issue. I do not think that a proper parameterization of the poly-unsaturated chains have been made, but I might be wrong. The 5 vs 6 beads might be that originally a 6 beads was used but was found a little too long compared to atomistic models but I can really remember.
I do remember using them for a project some time ago and we realized that multiple D beads in a tail was increasing their attraction to proteins and themselves a little more than expected but we did not really have exp data. The project never got to an end :((.
I would think that a 5 beads might be ok but be careful with the interaction strength, not thoroughly tested!
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- z.sichaib
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4 years 5 months ago #8346
by z.sichaib
Replied by z.sichaib on topic Martini lipid itp generator
Thanks a lot for your reply Xavier :))
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