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Protein-ligand
- imankatouzian
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4 years 1 month ago - 4 years 1 month ago #8440
by imankatouzian
Protein-ligand was created by imankatouzian
Good day,
I want to simulate the interaction of a protein with a molecule (ligand)
I am using the martini force field with the simulation time of more than 5 micro seconds
Is there a tutorial which can help me in this regard
Thanks
I want to simulate the interaction of a protein with a molecule (ligand)
I am using the martini force field with the simulation time of more than 5 micro seconds
Is there a tutorial which can help me in this regard
Thanks
Last edit: 4 years 1 month ago by imankatouzian.
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4 years 1 month ago - 4 years 1 month ago #8441
by imankatouzian
Replied by imankatouzian on topic Protein-ligand
.
Last edit: 4 years 1 month ago by imankatouzian.
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4 years 1 month ago #8442
by riccardo
Replied by riccardo on topic Protein-ligand
At the moment, such a tutorial is not there. We plan to make one in the near future (next few months). For the moment, you can start by creating a protein model (
www.cgmartini.nl/index.php/tutorials-gen...n-gmx5/proteins-gmx5
) and a model for the ligand(s) (
www.cgmartini.nl/index.php/tutorials-gen...ng-new-molecule-gmx5
), if you haven't done so yet.
I will also try to remember to post something on this thread once a protein-ligand binding tutorial will be available.
I will also try to remember to post something on this thread once a protein-ligand binding tutorial will be available.
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4 years 1 month ago #8444
by imankatouzian
Replied by imankatouzian on topic Protein-ligand
Dear riccardo,
Many thanks for your response.
I have a small molecule which I want to simulate it using CG, should I apply the above-mentioned tutorial you sent me or is there another means to do it since the lipid in the tutorial was a biopolymer and a big molecule.
Thanks
Many thanks for your response.
I have a small molecule which I want to simulate it using CG, should I apply the above-mentioned tutorial you sent me or is there another means to do it since the lipid in the tutorial was a biopolymer and a big molecule.
Thanks
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- riccardo
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4 years 1 month ago - 4 years 1 month ago #8449
by riccardo
Replied by riccardo on topic Protein-ligand
I don't understand this last part of your post "since the lipid in the tutorial was a biopolymer and a big molecule"?
The tutorial I linked above for the parametrization of small molecules is what you need if your ligand is an arbitrary small molecule. If you suspect that your ligand is very similar to a topology which may be listed among the topologies available in the Downloads section ( cgmartini.nl/index.php/force-field-parameters ), please check that out carefully. If you find even only fragments of your molecule for which a Martini model already exist, you can start to build from there.
*EDIT: There was a typo, now corrected ("If you find...")
The tutorial I linked above for the parametrization of small molecules is what you need if your ligand is an arbitrary small molecule. If you suspect that your ligand is very similar to a topology which may be listed among the topologies available in the Downloads section ( cgmartini.nl/index.php/force-field-parameters ), please check that out carefully. If you find even only fragments of your molecule for which a Martini model already exist, you can start to build from there.
*EDIT: There was a typo, now corrected ("If you find...")
Last edit: 4 years 1 month ago by riccardo.
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4 years 1 month ago #8450
by imankatouzian
Replied by imankatouzian on topic Protein-ligand
Many thanks for your kind response riccardo.
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- riccardo
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3 years 6 months ago #8693
by riccardo
Replied by riccardo on topic Protein-ligand
We published a tutorial regarding protein-ligand binding simulations (with Martini 3). Please see here:
cgmartini.nl/index.php/martini-3-tutoria...all-molecule-binding
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