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Covalently attached Non-standard residue in the CG model
- aashuph16221
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2 years 10 months ago #8957
by aashuph16221
Covalently attached Non-standard residue in the CG model was created by aashuph16221
Dear CG martini community.
I am investigating the oligomer protein assembly through molecular dynamics simulation.
My protein has Heme and other non-standard residues.
I am using an amber force field. I have done successfully an all-atom molecular dynamics simulation.
I want to know how can generate the CG model for my complete system.
when I using the martinize.py script it generates only standard amino acid.
Can you guide me on how can generate the force field parameter of other covalently attached non-standard residues?
Kindly guide me
Best regards
Aashish
I am investigating the oligomer protein assembly through molecular dynamics simulation.
My protein has Heme and other non-standard residues.
I am using an amber force field. I have done successfully an all-atom molecular dynamics simulation.
I want to know how can generate the CG model for my complete system.
when I using the martinize.py script it generates only standard amino acid.
Can you guide me on how can generate the force field parameter of other covalently attached non-standard residues?
Kindly guide me
Best regards
Aashish
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- riccardo
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2 years 10 months ago #8960
by riccardo
Replied by riccardo on topic Covalently attached Non-standard residue in the CG model
You should look for - or parametrize from scratch - a Martini model for the non-standard residues.
You mention Heme so have a look at, for example: pubs.acs.org/doi/abs/10.1021/acs.jpcb.5b00809
and
www.sciencedirect.com/science/article/pii/S000634951930195X .
To parametrize non-standard residues from scratch:
Martini 2: www.cgmartini.nl/index.php/tutorials-gen...ng-new-molecule-gmx5
Martini 3: www.cgmartini.nl/index.php/martini-3-tut...a-new-small-molecule
Of course, I recommend using Martini 3 ( www.nature.com/articles/s41592-021-01098-3 ), especially because you're looking at protein-protein interactions.
Once you have the models of the non-standard residues, you need to attach them "by hand" to the protein, i.e., add bonds/angles between those residues and the amino acids in the topology. Maybe you can also do it in a more automated way with Martinize2 ( github.com/marrink-lab/vermouth-martinize ); the documentation is still a bit scarce but hopefully this is gonna get fixed soon; there's some documentation in the SI of www.nature.com/articles/s41592-021-01098-3 .
You mention Heme so have a look at, for example: pubs.acs.org/doi/abs/10.1021/acs.jpcb.5b00809
and
www.sciencedirect.com/science/article/pii/S000634951930195X .
To parametrize non-standard residues from scratch:
Martini 2: www.cgmartini.nl/index.php/tutorials-gen...ng-new-molecule-gmx5
Martini 3: www.cgmartini.nl/index.php/martini-3-tut...a-new-small-molecule
Of course, I recommend using Martini 3 ( www.nature.com/articles/s41592-021-01098-3 ), especially because you're looking at protein-protein interactions.
Once you have the models of the non-standard residues, you need to attach them "by hand" to the protein, i.e., add bonds/angles between those residues and the amino acids in the topology. Maybe you can also do it in a more automated way with Martinize2 ( github.com/marrink-lab/vermouth-martinize ); the documentation is still a bit scarce but hopefully this is gonna get fixed soon; there's some documentation in the SI of www.nature.com/articles/s41592-021-01098-3 .
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