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CG Protein- Ligand complex
- Romero
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9 years 6 months ago #4097
by Romero
CG Protein- Ligand complex was created by Romero
Dear all,
I am trying to simulate a protein bounded to its ligand using Martini FF.
I have atomistic parameters for the complex and cg parameters for both protein and ligand (which is a lipid) separately, both are stable when simulates separately, but i do not really know how to bring both together in order to perform a cg md simulation of the complex over a lipid membrane.
Can anyone help me?
Thanks a lot!
I am trying to simulate a protein bounded to its ligand using Martini FF.
I have atomistic parameters for the complex and cg parameters for both protein and ligand (which is a lipid) separately, both are stable when simulates separately, but i do not really know how to bring both together in order to perform a cg md simulation of the complex over a lipid membrane.
Can anyone help me?
Thanks a lot!
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- helgi
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9 years 6 months ago #4099
by helgi
Replied by helgi on topic CG Protein- Ligand complex
Hello, hello,
The right way to do this can very somewhat depending on your specific case (protein-ligand in question), but generally if you have an atomistic structure of the complex and a CG force field of both you can use martinize.py to get the CG structure file for the protein. Then you can simple pick coordinates for you bound ligand/lipid that are close to the center of mass the of the underlying mapped atoms (for example by picking the AA atoms that are close to the middle of each bead – at the CG level a small ligand/lipid is normally only a few atoms so doing this by hand is not so much work then you minimize the structures together, with position restraints on the protein and not the ligand, and you should get the proper complex at the CG level). Alternatively you can use a tool such as backwards ( cgmartini.nl/cgmartini/index.php/others#Backward ), it can also forwards maps structures but you will have to define the mapping files for your molecules.
Next, you would insert the complex into a bilayer using for example insane.py
Hope this helps,
Cheers,
- Helgi
The right way to do this can very somewhat depending on your specific case (protein-ligand in question), but generally if you have an atomistic structure of the complex and a CG force field of both you can use martinize.py to get the CG structure file for the protein. Then you can simple pick coordinates for you bound ligand/lipid that are close to the center of mass the of the underlying mapped atoms (for example by picking the AA atoms that are close to the middle of each bead – at the CG level a small ligand/lipid is normally only a few atoms so doing this by hand is not so much work then you minimize the structures together, with position restraints on the protein and not the ligand, and you should get the proper complex at the CG level). Alternatively you can use a tool such as backwards ( cgmartini.nl/cgmartini/index.php/others#Backward ), it can also forwards maps structures but you will have to define the mapping files for your molecules.
Next, you would insert the complex into a bilayer using for example insane.py
Hope this helps,
Cheers,
- Helgi
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- Romero
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9 years 5 months ago #4132
by Romero
Replied by Romero on topic CG Protein- Ligand complex
Thanks Helgi!
Actually, it was quite straightforward with your instructions,
However when i just put the possitions restrains over the protein the lipid escaped from the binding site and got hiden among the molecules of DPPC of the lipid membrane, after few steps of the simulation.
Does anyone have any sugestion for this???
Thanks a lot in advance,
Cheers
Raquel
Actually, it was quite straightforward with your instructions,
However when i just put the possitions restrains over the protein the lipid escaped from the binding site and got hiden among the molecules of DPPC of the lipid membrane, after few steps of the simulation.
Does anyone have any sugestion for this???
Thanks a lot in advance,
Cheers
Raquel
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- helgi
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9 years 5 months ago #4133
by helgi
Replied by helgi on topic CG Protein- Ligand complex
Hello, hello,
You can do this in a number of ways. If you just want to keep them together initially (during minimization / equilibration) the easiest would be just to put a week position restrain on the lipid headgroup (you can even use the same if/def flag that is used for the protein then removing the –D flag in your .mdp file would remove both). Alternatively if this is a bounded ligand (e.g. makes a disulfide bonds or stuck for some other reason) you could merge the .itp of the protein and the lipid (just be careful to update the atom numbers) and link them with a bond.
Cheers,
- Helgi
You can do this in a number of ways. If you just want to keep them together initially (during minimization / equilibration) the easiest would be just to put a week position restrain on the lipid headgroup (you can even use the same if/def flag that is used for the protein then removing the –D flag in your .mdp file would remove both). Alternatively if this is a bounded ligand (e.g. makes a disulfide bonds or stuck for some other reason) you could merge the .itp of the protein and the lipid (just be careful to update the atom numbers) and link them with a bond.
Cheers,
- Helgi
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- MOURI
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7 years 5 months ago #6000
by MOURI
Replied by MOURI on topic CG Protein- Ligand complex
Hi
I want to use distance restraint between two proteins in gromacs. My proteins are very far away from each other.
I am confused with the problem.
Anyone have any ideas?
Best Regards
Mouri
I want to use distance restraint between two proteins in gromacs. My proteins are very far away from each other.
I am confused with the problem.
Anyone have any ideas?
Best Regards
Mouri
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- peterkroon
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7 years 5 months ago #6002
by peterkroon
Replied by peterkroon on topic CG Protein- Ligand complex
Hi,
I'd use the Gromacs pull code with a pull-rate of 0. See manual.gromacs.org/documentation/5.1/use...ons.html#com-pulling
Peter
I'd use the Gromacs pull code with a pull-rate of 0. See manual.gromacs.org/documentation/5.1/use...ons.html#com-pulling
Peter
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- MOURI
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7 years 5 months ago #6280
by MOURI
Replied by MOURI on topic CG Protein- Ligand complex
Thanks for the help Sir.
Best Regards
Mouri
Best Regards
Mouri
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