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normal Creating MARTINI Topology for Organic Ligand

  • yipy0005
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9 years 9 months ago #3955 by yipy0005
Creating MARTINI Topology for Organic Ligand was created by yipy0005
Hi, I wish to ask if it's possible to derive a martini topology of an organic ligand by ourselves? I'm trying a run a long time-scale simulation with a protein and a ligand included in it. Therefore, I'm planning to execute 2 strategies:

1. Run a CG MD with both the complex (meaning making the whole complex CG).
2. Run with the protein CG and the ligand AA (but I don't know how to do this, especially the part on generating the different topologies and merging together).

Please advise. Any help would be greatly appreciated. =)

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9 years 9 months ago #3956 by Clement
Replied by Clement on topic Creating MARTINI Topology for Organic Ligand

Hi, I wish to ask if it's possible to derive a martini topology of an organic ligand by ourselves?

We thought about your question! Check that out: md.chem.rug.nl/cgmartini/index.php/parametrzining-new-molecule .

I'm trying a run a long time-scale simulation with a protein and a ligand included in it. Therefore, I'm planning to execute 2 strategies:

1. Run a CG MD with both the complex (meaning making the whole complex CG).

No problem, as soon as you derive the topology of the molecule you need... Link above.

2. Run with the protein CG and the ligand AA (but I don't know how to do this, especially the part on generating the different topologies and merging together).

That's... tricky at best. But check our literature on the subject: scitation.aip.org/content/aip/journal/jc.../5/10.1063/1.4863329 and pubs.acs.org/doi/abs/10.1021/ct5001523 . You'll find plenty of other papers on that, look around. Good luck!

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9 years 9 months ago #3958 by yipy0005
Replied by yipy0005 on topic Creating MARTINI Topology for Organic Ligand
I tried the tutorial, it works great! I have a quick question to ask: the 1st step in the tutorial was to simulate toluene in the decane solvent. I visualize the gromos.xtc with gromos.gro after mdrun in VMD and the solvent seems to have long bonds. Is it normal for that?

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9 years 9 months ago #3959 by jaakko
Replied by jaakko on topic Creating MARTINI Topology for Organic Ligand

yipy0005 wrote: I visualize the gromos.xtc with gromos.gro after mdrun in VMD and the solvent seems to have long bonds. Is it normal for that?

VMD is probably drawing bonds for molecules that are partly over the periodic boundary. Run trjconv -pbc mol for your trajectory to make the solvent molecules whole.

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9 years 9 months ago #3960 by yipy0005
Replied by yipy0005 on topic Creating MARTINI Topology for Organic Ligand
Thanks jaakko, you are right indeed. Now I can't wait for you guys to come up with tutorial on how to verify the cg parameterizing of new molecule with experimental results. =)

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9 years 9 months ago #3961 by Clement
Replied by Clement on topic Creating MARTINI Topology for Organic Ligand
Do you have experimental quantities to compare to? What kind of data?

To check your parameterization, partition data (logP, between water/cyclohexane/octanol for instance) is the easiest. You can already check the general behavior of your newly parameterized molecule by simulating pure mixtures.

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9 years 9 months ago - 9 years 9 months ago #3962 by yipy0005
Replied by yipy0005 on topic Creating MARTINI Topology for Organic Ligand
I have the log p data, but how can I use it to check the general behaviour of my newly parameterized molecule?

On the other hand, do you have any papers to recommend that I can look at, where other groups have tried parameterizing new molecules with the martini force field?

=)
Last edit: 9 years 9 months ago by yipy0005.

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9 years 9 months ago #3965 by siewert
Replied by siewert on topic Creating MARTINI Topology for Organic Ligand
The following two papers provide good examples of parameterization with the Martini force field:

C.A. Lopez, A. Rzepiela, A.H. de Vries, L. Dijkhuizen, P.H. Huenenberger, S.J. Marrink. The Martini coarse grained force field: extension to carbohydrates. J. Chem. Th. Comp., 5:3195-3210, 2009.

D.H. de Jong, G. Singh, W.F.D. Bennett, C. Arnarez, T.A. Wassenaar, L.V. Schäfer, X. Periole, D.P. Tieleman, S.J. Marrink. Improved parameters for the Martini coarse-grained protein force field, JCTC, 9:687–697, 2013.

Good luck!

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