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phosphatidylcholine
- syahidah
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13 years 1 month ago #615
by syahidah
phosphatidylcholine was created by syahidah
greeting everyone,
forgive me for this questions. i am so new with the cgmd.fyi, i want to do coarse grained structure for phosphatidylcholine surfactant structure. by referring to the table 3 which provided in Marrink's paper (the MARTINI force field for biomolecular simulation)that give us the guide to do the mapping process,i do know how to choose the region of the structure to be in 1 bead and its types, however, i don't know how to prepare it in the format that required by gromacs to do the cgmd simulation. so, may i know how can we prepare the coarse grained structure from the scratch structure.if possible, would anyone share with me the protocols to prepare the surfactant (eg:phosphatidylcholine) structure from scratch until we get the files that required by cgmd simulation (eg: .gro, .top, etc)
thank you,
best,
nurul
forgive me for this questions. i am so new with the cgmd.fyi, i want to do coarse grained structure for phosphatidylcholine surfactant structure. by referring to the table 3 which provided in Marrink's paper (the MARTINI force field for biomolecular simulation)that give us the guide to do the mapping process,i do know how to choose the region of the structure to be in 1 bead and its types, however, i don't know how to prepare it in the format that required by gromacs to do the cgmd simulation. so, may i know how can we prepare the coarse grained structure from the scratch structure.if possible, would anyone share with me the protocols to prepare the surfactant (eg:phosphatidylcholine) structure from scratch until we get the files that required by cgmd simulation (eg: .gro, .top, etc)
thank you,
best,
nurul
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- xavier
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13 years 1 month ago #617
by xavier
Replied by xavier on topic phosphatidylcholine
You could look at other molecules like regular lipids to see how the things are done and you could probably find other molecules that look like your surfactant among the lipids defined.
The files are available on the download section of the website.
XAvier.
The files are available on the download section of the website.
XAvier.
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- syahidah
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13 years 4 weeks ago #623
by syahidah
Replied by syahidah on topic phosphatidylcholine
GREETING EVERYONE,
i was thinking that may i build an all-atom structure, meaning that, i build an all-atom structure from scratch:
i draw the structure in avogadro and save it in pdb file. then, i use it to produce .gro&topology files by using antechamber.can all-atom*.gro&topology converted to cg*.gro&cg topology files?is there any command like the one that being used for protein to convert this?
sorry for this silly question,
best,
nurul
i was thinking that may i build an all-atom structure, meaning that, i build an all-atom structure from scratch:
i draw the structure in avogadro and save it in pdb file. then, i use it to produce .gro&topology files by using antechamber.can all-atom*.gro&topology converted to cg*.gro&cg topology files?is there any command like the one that being used for protein to convert this?
sorry for this silly question,
best,
nurul
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- xavier
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13 years 4 weeks ago #624
by xavier
There is no automatic conversion script for lipids or random molecules. You have to do it by hand inspiring yourself from examples or go through the reverse transformation gromacs version. In the latter case you should go through the tutorial.
XAvier
Replied by xavier on topic phosphatidylcholine
syahidah wrote: GREETING EVERYONE,
i was thinking that may i build an all-atom structure, meaning that, i build an all-atom structure from scratch:
i draw the structure in avogadro and save it in pdb file. then, i use it to produce .gro&topology files by using antechamber.can all-atom*.gro&topology converted to cg*.gro&cg topology files?is there any command like the one that being used for protein to convert this?
sorry for this silly question,
best,
nurul
There is no automatic conversion script for lipids or random molecules. You have to do it by hand inspiring yourself from examples or go through the reverse transformation gromacs version. In the latter case you should go through the tutorial.
XAvier
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