normal PMF of protein dimerization using MARTINI3 forcefield

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2 years 11 months ago #8958 by ayan95
Hi,

I was trying to reproduce the published dimerization energy value for GpA and EphA1 by using the MARTINI3 forcefield.

It seems like my results are deviating by a large number for both cases. I am not using the flexible protein model.

I am still not able to equilibrate the bilayer with the flexible model. It is giving linc error for a few protein beads.

Thanks,
Ayan

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2 years 11 months ago #8961 by riccardo
Be sure to follow the same protocol as stated in www.nature.com/articles/s41592-021-01098-3 and you should be OK.
How large is large?

What do you mean by flexible model?

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2 years 11 months ago #8966 by ayan95
I am using the same protocol as mentioned in the MARTINI3 paper, i.e., I am using the new-RF mdp file.

Q. How large is large?

The PMF depth of GpA is off by ~10 kJ/mol (I am getting more like MARTINI2 result) and EphA1 is off by 7 kJ/mol.

Q. What do you mean by flexible model?

In the martinize2 protein itp file. I see you guys included two options for sidechain parameter. One is flexible with sidechain beads interactions included in the bonded parameter. One like previous (#ifndef FLEXIBLE), sidechain beads are constrained.

Please let me know if I can share any files. Maybe through emails.

Thanks,
Ayan

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