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Protein-Ligand CG MD simulation
- z.sichaib
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6 years 2 months ago #7548
by z.sichaib
Protein-Ligand CG MD simulation was created by z.sichaib
Hi,
I have a protein-ligand complex (dimer) that I would like to simulate using MARTINI FF and GROMACS software.
The ligand is a small molecule of 352,856 Da. I have its all-atom topology from a previous project. it was generated using The General Amber force field (GAFF) parameters, along with the RESP atomic charge fitted with the electrostatic potential (ESP) from Gaussian 09 calculation with the HF-6-31G* basis set. The topology was then converted to GROMACS format using the ACPYPE tool.
Since I'm new in Martini, I would like to know how can I proceed with the ligand in order to generate its CG topology since it's not parametrized in it? Are there any tutorials for Protein-Ligand MARTINI CG?
Thank you in advance for your help.
Best,
I have a protein-ligand complex (dimer) that I would like to simulate using MARTINI FF and GROMACS software.
The ligand is a small molecule of 352,856 Da. I have its all-atom topology from a previous project. it was generated using The General Amber force field (GAFF) parameters, along with the RESP atomic charge fitted with the electrostatic potential (ESP) from Gaussian 09 calculation with the HF-6-31G* basis set. The topology was then converted to GROMACS format using the ACPYPE tool.
Since I'm new in Martini, I would like to know how can I proceed with the ligand in order to generate its CG topology since it's not parametrized in it? Are there any tutorials for Protein-Ligand MARTINI CG?
Thank you in advance for your help.
Best,
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- Pim
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6 years 1 month ago #7554
by Pim
Replied by Pim on topic Protein-Ligand CG MD simulation
Parametrizing a protein with a ligand is much the same as the two separate. Parametrization of the protein can be done using the martinize.py script, probably with an elastic network. Parametrizing the ligand can be done using the tutorial
cgmartini.nl/index.php/tutorials-general...ng-new-molecule-gmx5
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If your ligand is really 352856 Dalton, I wouldn't say it's small, that's a massive molecule! If you mean 352.856 Da I guess you're fine, just follow the tutorial.
If you have managed both, you might have to connect your ligand to your protein via restraints or bonds if it doesn't stay there by itself. We've regularly seen cofactors diffuse out of their binding pocket due to the CG nature of the complex. I think the best and most complete example of a protein complex with many ligands/cofactors is the PSII complex, you can find all the details of its parametrization here: pubs.acs.org/doi/full/10.1021/acs.jpcb.6b06865
If you're trying to study ligand binding, you obviously should not connect protein and ligand, but you would have to be a bit lucky to see such a process using a CG force field.
If your ligand is really 352856 Dalton, I wouldn't say it's small, that's a massive molecule! If you mean 352.856 Da I guess you're fine, just follow the tutorial.
If you have managed both, you might have to connect your ligand to your protein via restraints or bonds if it doesn't stay there by itself. We've regularly seen cofactors diffuse out of their binding pocket due to the CG nature of the complex. I think the best and most complete example of a protein complex with many ligands/cofactors is the PSII complex, you can find all the details of its parametrization here: pubs.acs.org/doi/full/10.1021/acs.jpcb.6b06865
If you're trying to study ligand binding, you obviously should not connect protein and ligand, but you would have to be a bit lucky to see such a process using a CG force field.
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