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Mutating residues in martini forcefield
- rcorey
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8 years 11 months ago #4562
by rcorey
Mutating residues in martini forcefield was created by rcorey
Hello
Does anyone know of a program (GUI or command line) which is able to take a martini protein model and mutate one or more residues within it?A bit like Scwrl4 perhaps, but applicable for coarse grain forcefields.
Many thanks
Robin
Does anyone know of a program (GUI or command line) which is able to take a martini protein model and mutate one or more residues within it?A bit like Scwrl4 perhaps, but applicable for coarse grain forcefields.
Many thanks
Robin
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- Clement
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8 years 10 months ago #4588
by Clement
Replied by Clement on topic Mutating residues in martini forcefield
What about... mutating the atomistic structure and re-generate an .itp for it? Just as fast...
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- rcorey
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8 years 10 months ago #4589
by rcorey
Replied by rcorey on topic Mutating residues in martini forcefield
Thanks for the response.
Yes - this is what I was going to try but isn't ideal; I want to convert an atomistic model to coarse grain, run a martini simulation, mutate a residue, run a new martini simulation, mutate another residue etc etc. I fear that going from atomistic to coarse grain to atomistic to coarse grain multiple times might lead to issues (especially as I'm trying to detect specific protein-lipid interactions).
Yes - this is what I was going to try but isn't ideal; I want to convert an atomistic model to coarse grain, run a martini simulation, mutate a residue, run a new martini simulation, mutate another residue etc etc. I fear that going from atomistic to coarse grain to atomistic to coarse grain multiple times might lead to issues (especially as I'm trying to detect specific protein-lipid interactions).
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- Clement
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8 years 10 months ago - 8 years 10 months ago #4590
by Clement
Replied by Clement on topic Mutating residues in martini forcefield
Why do you need to convert your CG structure to AA to get a new topology...? The topology of your protein isn't modified by your simulation. The topology of the mutated protein should be the same in each case; only the mutated residue would affect it a tidbit, locally.
I would recommend/advise generating your mutant topologies from your initial AA structure, the same you used to define your apo-topology; initial structure you mutate to taste, using the software you prefer. You can then add/remove manually a bead in the CG system if needed (add a bead to your conformation file, move it close to the mutated residue with VMD for instance), minimize again, and run. No need for gymnastics between CG and AA.
I would recommend/advise generating your mutant topologies from your initial AA structure, the same you used to define your apo-topology; initial structure you mutate to taste, using the software you prefer. You can then add/remove manually a bead in the CG system if needed (add a bead to your conformation file, move it close to the mutated residue with VMD for instance), minimize again, and run. No need for gymnastics between CG and AA.
Last edit: 8 years 10 months ago by Clement.
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- rcorey
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8 years 10 months ago #4593
by rcorey
Replied by rcorey on topic Mutating residues in martini forcefield
Oh - I see what you mean. Generate a new .itp based on mutated-atomistic and use that with the coarse grain coordinates (+/- beads).
Yes, not thought of it like that. That should work fine.
Thanks!
Yes, not thought of it like that. That should work fine.
Thanks!
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