- Posts: 2
Non-standard residues (PTR) in Martini FF
- Tam Nguyen
-
Topic Author
- Offline
- Fresh Boarder
Less
More
7 years 10 months ago #5637
by Tam Nguyen
Non-standard residues (PTR) in Martini FF was created by Tam Nguyen
I am simulating the protein with phosphotyrosine residues; however, this residue type is not defined in Martinize.py. Could you please tell me how to generate the coarse-grained model which has non-standard residues?
Thank you a lot!
Thank you a lot!
Please Log in or Create an account to join the conversation.
- bart
-
- Offline
- Admin
Less
More
- Posts: 98
7 years 9 months ago - 7 years 9 months ago #5724
by bart
Replied by bart on topic Non-standard residues (PTR) in Martini FF
Hello Tam,
As of yet this has to be done manually, though I think it could be a possible extension to Martinze to include post-translational modified residues.
If the phosphotyrosine is not hidden in the protein-core I would suggest to just replace it by tyrosine and than add the phosphogroup to it after you run Martinize (you probably only have to add one bead afterwards). To do so properly, it might be necessary to run some AA/UA simulations of the phosphotyrosine in solution to create a proper description of the residue. You could take a look at the mapping of the nucleotides in the DNA model to get a start for the mapping of the phosphate group. Here is a tutorial which could prove to be helpful for the parametrisation of a new molecule.
Cheers,
Bart
As of yet this has to be done manually, though I think it could be a possible extension to Martinze to include post-translational modified residues.
If the phosphotyrosine is not hidden in the protein-core I would suggest to just replace it by tyrosine and than add the phosphogroup to it after you run Martinize (you probably only have to add one bead afterwards). To do so properly, it might be necessary to run some AA/UA simulations of the phosphotyrosine in solution to create a proper description of the residue. You could take a look at the mapping of the nucleotides in the DNA model to get a start for the mapping of the phosphate group. Here is a tutorial which could prove to be helpful for the parametrisation of a new molecule.
Cheers,
Bart
Last edit: 7 years 9 months ago by bart.
Please Log in or Create an account to join the conversation.
- Tam Nguyen
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 2
7 years 9 months ago #5737
by Tam Nguyen
Replied by Tam Nguyen on topic Non-standard residues (PTR) in Martini FF
Thank you a lot for your help, Bart!
Please Log in or Create an account to join the conversation.
- siewert
-
- Offline
- Admin
Less
More
- Posts: 61
7 years 9 months ago #5738
by siewert
Replied by siewert on topic Non-standard residues (PTR) in Martini FF
A good initial model would be adding a Qa particle with a double negative charge (representing the charged state of phosphate a neutral pH), attached to a PHE residue (not a TYR, as the hydroxyl group is now adsorbed into the phosphate bead) with a bond length corresponding to the center of mass distance of the respective groups (and a standard force constant of around 5000 as used in other amino acids).
Depending on your application (i.e. whether or not the phosphotyrosine plays a central role), you could try to optimize the model using atomistic simulations as Bart already suggested.
Depending on your application (i.e. whether or not the phosphotyrosine plays a central role), you could try to optimize the model using atomistic simulations as Bart already suggested.
Please Log in or Create an account to join the conversation.
Time to create page: 0.104 seconds